Reproducible microbial GWAS from paired-end reads for one explicitly coded binary phenotype per run, including gene presence/absence GWAS, optional SNP marker GWAS, population-structure visualization, post-GWAS reference annotation, and ranked association reporting.
rpoB_763031_T_C_marker_present_vs_absent. Configured contrast: case (rpoB 763031 T C present) versus control (rpoB 763031 T C absent). The report displays the metadata-derived biological contrast throughout the HTML: case (rpoB 763031 T C present) = 1 and control (rpoB 763031 T C absent) = 0.| Class | Pyseer coding | Metadata column | Metadata value used for display | Samples | Report label |
|---|---|---|---|---|---|
| case | 1 | rpoB_763031_T_C_marker_present_vs_absent | rpoB 763031 T C present | 50 | case (rpoB 763031 T C present) |
| control | 0 | rpoB_763031_T_C_marker_present_vs_absent | rpoB 763031 T C absent | 50 | control (rpoB 763031 T C absent) |
| Interpretation issue | Current workflow/report behavior | Recommended interpretation |
|---|---|---|
| Phenotype clarity | One binary phenotype is tested per run using the phenotype TSV supplied to pyseer. | Use phenotype_name and phenotype_display_values to show the real biological contrast, for example specimen_source, HIV_status, MRSA_vs_MSSA, or rpoB_marker_status. |
| Gene presence/absence | The primary GWAS branch tests pangenome gene-cluster presence/absence with population-structure correction. | Interpret hits as gene-cluster associations with the configured phenotype, not as resistance genes unless the phenotype is explicitly an AMR contrast. |
| Point mutations | Point mutations are assessed only when the optional SNP GWAS branch is enabled. | Use do_snp_gwas=true for marker-defined or mutation-driven contrasts, then interpret SNP hits against the configured case/control labels. |
| Sample metadata and sampling design | The report displays the metadata-derived case/control labels, but metadata columns are not automatically modeled as covariates. | For phenotypes such as specimen source, HIV status, geography, host category, or marker carriage, check whether lineage, site, or sampling design explains the association. |
| Sequencing depth and assembly quality | The workflow generates FASTQ/assembly QC outputs, but read depth and assembly quality are not automatically modeled as covariates. | Filter low-depth or poor-quality samples and confirm that apparent gene absence is not caused by technical dropout. |
| Population structure and linkage | Mash distances/MDS and population-structure plots are generated to help assess lineage confounding. | If the configured phenotype clusters by lineage or outbreak, treat hits as candidate associations requiring validation rather than causal determinants. |
Checks sample names, paired FASTQs, group labels, and case (rpoB 763031 T C present)/control (rpoB 763031 T C absent) balance.
Generates cleaned reads plus QC summaries.
Builds de novo genome assemblies using safe Cromwell memory handling.
Creates GFF annotations and pangenome gene matrices. Prokka remains the default; Bakta can be enabled with use_bakta=true.
Runs population-structure-aware gene and optional SNP association testing.
Maps prioritized pangenome/SNP markers to reference GenBank features where possible.
metric value phenotype rpoB_763031_T_C_marker_present_vs_absent case_label case (rpoB 763031 T C present) (rpoB 763031 T C present) control_label control (rpoB 763031 T C absent) (rpoB 763031 T C absent) samples 100 pcoa1_variance_percent 93.2973 pcoa2_variance_percent 1.4895 pcoa1_plus_pcoa2_variance_percent 94.7867 case_within_mean_mash_distance 0.0013734307307755103 control_within_mean_mash_distance 0.0009351074274285714 between_group_mean_mash_distance 0.0014321130195999998 between_within_mash_distance_ratio 1.2407 pcoa_centroid_separation_score 0.5039 method PCoA from square Mash distance matrix plus distance heatmap layman_pcoa_interpretation The PCoA plot shows moderate separation between the two phenotype groups (PCoA separation score 0.50; between/within Mash distance ratio 1.24). Some GWAS signals may still be influenced by lineage, so prioritize hits that remain biologically plausible and are not explained only by clustering.
metric value pvalues_detected 1424 points_drawn 1424 plot_label Gene presence/absence GWAS significant_points_at_alpha 178 top_feature group_3150 top_pvalue 3.46e-16 top_minus_log10_pvalue 15.4609 qq_median_delta_observed_minus_expected -0.3013 qq_tail_delta_observed_minus_expected 12.0064 manhattan_type feature_index_not_genomic_coordinate qq_plot generated layman_manhattan_interpretation Each dot is a gene or gene cluster. Taller dots mean stronger evidence of difference between the two groups. In this run, 178 of 1424 tested gene features crossed the alpha=0.05 line. The tallest signal was group_3150 (p=3.46e-16). Multiple significant dots may represent linked genes, mobile elements, or lineage effects, so review the priority table and population structure before interpreting them as independent causal markers. layman_qq_interpretation Most QQ-plot points are close to the expected background, but the upper tail rises above expectation. That pattern is consistent with a small number of candidate gene associations rather than general inflation. The candidate signals should still be checked against population structure and annotation confidence.
metric value plot_label SNP marker GWAS pvalues_detected 17248 significant_points_at_alpha 1798 top_marker NC_000962.3_15117_C_G top_position 15117 top_pvalue 4.54e-18 top_minus_log10_pvalue 17.3429 qq_median_delta_observed_minus_expected -0.3011 qq_tail_delta_observed_minus_expected 12.8052 points_drawn 5000 manhattan_type reference_coordinate_when_available qq_plot generated layman_manhattan_interpretation Each dot is a SNP marker placed by reference coordinate when available. 1798 of 17248 tested SNP markers crossed the alpha=0.05 line. The strongest marker was NC_000962.3_15117_C_G at position 15117 (p=4.54e-18). Clusters of SNP hits can reflect true mutation signal, lineage background, or linked variants, so review the top-hit table and PCoA/kinship plots before interpretation. layman_qq_interpretation The SNP QQ plot has a raised upper tail with less broad inflation across the rest of the plot. This pattern is compatible with a limited number of candidate SNP associations, but they still need biological validation and lineage checks.
anthranilate synthase component II
transmembrane protein
transmembrane protein
hypothetical protein
oxalyl-CoA decarboxylase OxcA
| rank | feature id | variant id | feature type | contig | position | ref | alt | gene name | product | reference locus tag | reference gene | reference product | case (rpoB 763031 T C present) alt | case (rpoB 763031 T C present) total | case (rpoB 763031 T C present) frequency | control (rpoB 763031 T C absent) alt | control (rpoB 763031 T C absent) total | control (rpoB 763031 T C absent) frequency | enriched in | beta | odds ratio | odds ratio ci95 | odds ratio ci95 lower | odds ratio ci95 upper | pyseer pvalue | q value | priority score | annotation source | reference location | qual | notes |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | NC_000962.3_15117_C_G | NC_000962.3_15117_C_G | snp | NC_000962.3 | 15117 | C | G | trpG | anthranilate synthase component II | Rv0013 | trpG | anthranilate synthase component II | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 14914..15612 | 11107.4 | SNP-level association; inspect population structure before causal interpretation. | |
| 2 | NC_000962.3_42281_C_A | NC_000962.3_42281_C_A | snp | NC_000962.3 | 42281 | C | A | Rv0039c | transmembrane protein | Rv0039c | transmembrane protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(42004..42351) | 10156.1 | SNP-level association; inspect population structure before causal interpretation. | ||
| 3 | NC_000962.3_70267_G_T | NC_000962.3_70267_G_T | snp | NC_000962.3 | 70267 | G | T | Rv0064 | transmembrane protein | Rv0064 | transmembrane protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 68620..71559 | 11080.5 | SNP-level association; inspect population structure before causal interpretation. | ||
| 4 | NC_000962.3_123520_T_C | NC_000962.3_123520_T_C | snp | NC_000962.3 | 123520 | T | C | Rv0104 | hypothetical protein | Rv0104 | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 122317..123831 | 11226.7 | SNP-level association; inspect population structure before causal interpretation. | ||
| 5 | NC_000962.3_143207_T_C | NC_000962.3_143207_T_C | snp | NC_000962.3 | 143207 | T | C | oxcA | oxalyl-CoA decarboxylase OxcA | Rv0118c | oxcA | oxalyl-CoA decarboxylase OxcA | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(142128..143876) | 10156.3 | SNP-level association; inspect population structure before causal interpretation. | |
| 6 | NC_000962.3_199470_T_G | NC_000962.3_199470_T_G | snp | NC_000962.3 | 199470 | T | G | mce1A | Mce family protein Mce1A | Rv0169 | mce1A | Mce family protein Mce1A | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 198534..199898 | 10240.8 | SNP-level association; inspect population structure before causal interpretation. | |
| 7 | NC_000962.3_217201_T_C | NC_000962.3_217201_T_C | snp | NC_000962.3 | 217201 | T | C | bglS | beta-glucosidase BglS | Rv0186 | bglS | beta-glucosidase BglS | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 216269..218344 | 9570.31 | SNP-level association; inspect population structure before causal interpretation. | |
| 8 | NC_000962.3_249522_T_C | NC_000962.3_249522_T_C | snp | NC_000962.3 | 249522 | T | C | Rv0209 | hypothetical protein | Rv0209 | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 249038..250123 | 9351.3 | SNP-level association; inspect population structure before causal interpretation. | ||
| 9 | NC_000962.3_251575_G_A | NC_000962.3_251575_G_A | snp | NC_000962.3 | 251575 | G | A | Rv0210 | hypothetical protein | Rv0210 | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 250120..251598 | 10212.6 | SNP-level association; inspect population structure before causal interpretation. | ||
| 10 | NC_000962.3_325505_T_C | NC_000962.3_325505_T_C | snp | NC_000962.3 | 325505 | T | C | fadD2 | fatty-acid--CoA ligase FadD2 | Rv0270 | fadD2 | fatty-acid--CoA ligase FadD2 | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 324567..326249 | 8015.75 | SNP-level association; inspect population structure before causal interpretation. | |
| 11 | NC_000962.3_342146_A_C | NC_000962.3_342146_A_C | snp | NC_000962.3 | 342146 | A | C | eccA3 | ESX-3 secretion system protein EccA | Rv0282 | eccA3 | ESX-3 secretion system protein EccA | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 342130..344025 | 11488.5 | SNP-level association; inspect population structure before causal interpretation. | |
| 12 | NC_000962.3_392261_T_C | NC_000962.3_392261_T_C | snp | NC_000962.3 | 392261 | T | C | Rv0325 | hypothetical protein | Rv0325 | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 392039..392263 | 10067.7 | SNP-level association; inspect population structure before causal interpretation. | ||
| 13 | NC_000962.3_445780_C_T | NC_000962.3_445780_C_T | snp | NC_000962.3 | 445780 | C | T | Rv0368c | hypothetical protein | Rv0368c | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(445314..446525) | 9884.36 | SNP-level association; inspect population structure before causal interpretation. | ||
| 14 | NC_000962.3_491742_T_C | NC_000962.3_491742_T_C | snp | NC_000962.3 | 491742 | T | C | fgd1 | F420-dependent glucose-6-phosphatedehydrogenase | Rv0407 | fgd1 | F420-dependent glucose-6-phosphatedehydrogenase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 490783..491793 | 11763.3 | SNP-level association; inspect population structure before causal interpretation. | |
| 15 | NC_000962.3_492150_G_C | NC_000962.3_492150_G_C | snp | NC_000962.3 | 492150 | G | C | pta | phosphate acetyltransferase | Rv0408 | pta | phosphate acetyltransferase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 491786..493858 | 10485.6 | SNP-level association; inspect population structure before causal interpretation. | |
| 16 | NC_000962.3_498531_A_G | NC_000962.3_498531_A_G | snp | NC_000962.3 | 498531 | A | G | Rv0412c | membrane protein | Rv0412c | membrane protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(498300..499619) | 10011 | SNP-level association; inspect population structure before causal interpretation. | ||
| 17 | NC_000962.3_517358_T_C | NC_000962.3_517358_T_C | snp | NC_000962.3 | 517358 | T | C | Rv0428c | GCN5-like N-acetyltransferase | Rv0428c | GCN5-like N-acetyltransferase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(516895..517803) | 9818.85 | SNP-level association; inspect population structure before causal interpretation. | ||
| 18 | NC_000962.3_546357_A_G | NC_000962.3_546357_A_G | snp | NC_000962.3 | 546357 | A | G | echA2 | enoyl-CoA hydratase EchA2 | Rv0456c | echA2 | enoyl-CoA hydratase EchA2 | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(545889..546803) | 9399.13 | SNP-level association; inspect population structure before causal interpretation. | |
| 19 | NC_000962.3_555991_A_G | NC_000962.3_555991_A_G | snp | NC_000962.3 | 555991 | A | G | Rv0465c | HTH-type transcriptional regulator | Rv0465c | HTH-type transcriptional regulator | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(554882..556306) | 10459 | SNP-level association; inspect population structure before causal interpretation. | ||
| 20 | NC_000962.3_584171_T_C | NC_000962.3_584171_T_C | snp | NC_000962.3 | 584171 | T | C | Rv0493c | hypothetical protein | Rv0493c | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(583701..584690) | 8967.48 | SNP-level association; inspect population structure before causal interpretation. | ||
| 21 | NC_000962.3_599868_A_G | NC_000962.3_599868_A_G | snp | NC_000962.3 | 599868 | A | G | mmpL2 | transmembrane transport protein MmpL2 | Rv0507 | mmpL2 | transmembrane transport protein MmpL2 | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 597199..600105 | 11944.2 | SNP-level association; inspect population structure before causal interpretation. | |
| 22 | NC_000962.3_648856_T_C | NC_000962.3_648856_T_C | snp | NC_000962.3 | 648856 | T | C | mgtA | GDP-mannose-dependent alpha-mannosyltransferase | Rv0557 | mgtA | GDP-mannose-dependent alpha-mannosyltransferase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 648536..649672 | 10465.8 | SNP-level association; inspect population structure before causal interpretation. | |
| 23 | NC_000962.3_655986_T_G | NC_000962.3_655986_T_G | snp | NC_000962.3 | 655986 | T | G | NC_000962.3_655986_T_G | intergenic_or_unannotated | intergenic_or_unannotated | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 9613.88 | SNP-level association; inspect population structure before causal interpretation. | ||||
| 24 | NC_000962.3_659341_T_C | NC_000962.3_659341_T_C | snp | NC_000962.3 | 659341 | T | C | NC_000962.3_659341_T_C | intergenic_or_unannotated | intergenic_or_unannotated | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 11692.3 | SNP-level association; inspect population structure before causal interpretation. | ||||
| 25 | NC_000962.3_662911_T_C | NC_000962.3_662911_T_C | snp | NC_000962.3 | 662911 | T | C | nrdZ | vitamin B12-dependent ribonucleoside-diphosphatereductase | Rv0570 | nrdZ | vitamin B12-dependent ribonucleoside-diphosphatereductase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 661295..663373 | 10132.7 | SNP-level association; inspect population structure before causal interpretation. | |
| 26 | NC_000962.3_670545_G_A | NC_000962.3_670545_G_A | snp | NC_000962.3 | 670545 | G | A | Rv0576 | transcriptional regulator | Rv0576 | transcriptional regulator | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 669848..671152 | 8977.98 | SNP-level association; inspect population structure before causal interpretation. | ||
| 27 | NC_000962.3_690450_A_C | NC_000962.3_690450_A_C | snp | NC_000962.3 | 690450 | A | C | mce2C | Mce family protein Mce2C | Rv0591 | mce2C | Mce family protein Mce2C | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 689059..690504 | 8741.29 | SNP-level association; inspect population structure before causal interpretation. | |
| 28 | NC_000962.3_713310_T_C | NC_000962.3_713310_T_C | snp | NC_000962.3 | 713310 | T | C | galK | galactokinase | Rv0620 | galK | galactokinase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 712716..713807 | 8793.59 | SNP-level association; inspect population structure before causal interpretation. | |
| 29 | NC_000962.3_757182_A_G | NC_000962.3_757182_A_G | snp | NC_000962.3 | 757182 | A | G | atsD | arylsulfatase AtsD | Rv0663 | atsD | arylsulfatase AtsD | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 756137..758500 | 9624.26 | SNP-level association; inspect population structure before causal interpretation. | |
| 30 | NC_000962.3_763031_T_C | NC_000962.3_763031_T_C | snp | NC_000962.3 | 763031 | T | C | rpoB | DNA-directed RNA polymerase subunit beta | Rv0667 | rpoB | DNA-directed RNA polymerase subunit beta | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 759807..763325 | 10533.1 | SNP-level association; inspect population structure before causal interpretation. | |
| 31 | NC_000962.3_776100_G_A | NC_000962.3_776100_G_A | snp | NC_000962.3 | 776100 | G | A | mmpL5 | transmembrane transport protein MmpL5 | Rv0676c | mmpL5 | transmembrane transport protein MmpL5 | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(775586..778480) | 9823.66 | SNP-level association; inspect population structure before causal interpretation. | |
| 32 | NC_000962.3_820752_C_T | NC_000962.3_820752_C_T | snp | NC_000962.3 | 820752 | C | T | serA2 | D-3-phosphoglycerate dehydrogenase SerA | Rv0728c | serA2 | D-3-phosphoglycerate dehydrogenase SerA | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(820496..821476) | 10170.3 | SNP-level association; inspect population structure before causal interpretation. | |
| 33 | NC_000962.3_847995_T_C | NC_000962.3_847995_T_C | snp | NC_000962.3 | 847995 | T | C | NC_000962.3_847995_T_C | intergenic_or_unannotated | intergenic_or_unannotated | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 9868.61 | SNP-level association; inspect population structure before causal interpretation. | ||||
| 34 | NC_000962.3_931123_T_C | NC_000962.3_931123_T_C | snp | NC_000962.3 | 931123 | T | C | lpqQ | lipoprotein LpqQ | Rv0835 | lpqQ | lipoprotein LpqQ | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 930953..931597 | 10911.5 | SNP-level association; inspect population structure before causal interpretation. | |
| 35 | NC_000962.3_934611_G_T | NC_000962.3_934611_G_T | snp | NC_000962.3 | 934611 | G | T | NC_000962.3_934611_G_T | intergenic_or_unannotated | intergenic_or_unannotated | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 11757.4 | SNP-level association; inspect population structure before causal interpretation. | ||||
| 36 | NC_000962.3_941845_C_A | NC_000962.3_941845_C_A | snp | NC_000962.3 | 941845 | C | A | Rv0845 | sensor histidine kinase NarS | Rv0845 | sensor histidine kinase NarS | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 941190..942467 | 10328.1 | SNP-level association; inspect population structure before causal interpretation. | ||
| 37 | NC_000962.3_960367_A_G | NC_000962.3_960367_A_G | snp | NC_000962.3 | 960367 | A | G | Rv0862c | hypothetical protein | Rv0862c | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(960342..962612) | 9628.55 | SNP-level association; inspect population structure before causal interpretation. | ||
| 38 | NC_000962.3_1024346_A_G | NC_000962.3_1024346_A_G | snp | NC_000962.3 | 1024346 | A | G | Rv0918 | hypothetical protein | Rv0918 | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 1024211..1024687 | 10147.2 | SNP-level association; inspect population structure before causal interpretation. | ||
| 39 | NC_000962.3_1054784_C_G | NC_000962.3_1054784_C_G | snp | NC_000962.3 | 1054784 | C | G | Rv0945 | oxidoreductase | Rv0945 | oxidoreductase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 1054247..1055008 | 10543 | SNP-level association; inspect population structure before causal interpretation. | ||
| 40 | NC_000962.3_1080192_G_A | NC_000962.3_1080192_G_A | snp | NC_000962.3 | 1080192 | G | A | ctpV | copper-exporting ATPase | Rv0969 | ctpV | copper-exporting ATPase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 1078743..1081055 | 9931.11 | SNP-level association; inspect population structure before causal interpretation. | |
| 41 | NC_000962.3_1098523_T_A | NC_000962.3_1098523_T_A | snp | NC_000962.3 | 1098523 | T | A | mprB | two component histidine-proteinkinase/phosphatase MprB | Rv0982 | mprB | two component histidine-proteinkinase/phosphatase MprB | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 1097508..1099022 | 9588.79 | SNP-level association; inspect population structure before causal interpretation. | |
| 42 | NC_000962.3_1104690_T_G | NC_000962.3_1104690_T_G | snp | NC_000962.3 | 1104690 | T | G | Rv0987 | adhesion component ABC transporter permease | Rv0987 | adhesion component ABC transporter permease | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 1102542..1105109 | 15362.1 | SNP-level association; inspect population structure before causal interpretation. | ||
| 43 | NC_000962.3_1107940_A_C | NC_000962.3_1107940_A_C | snp | NC_000962.3 | 1107940 | A | C | Rv0990c | hypothetical protein | Rv0990c | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(1107443..1108099) | 8857.77 | SNP-level association; inspect population structure before causal interpretation. | ||
| 44 | NC_000962.3_1148259_A_G | NC_000962.3_1148259_A_G | snp | NC_000962.3 | 1148259 | A | G | NC_000962.3_1148259_A_G | intergenic_or_unannotated | intergenic_or_unannotated | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 10384.3 | SNP-level association; inspect population structure before causal interpretation. | ||||
| 45 | NC_000962.3_1211369_A_C | NC_000962.3_1211369_A_C | snp | NC_000962.3 | 1211369 | A | C | Rv1086 | (2Z,6E)-farnesyl diphosphate synthase | Rv1086 | (2Z,6E)-farnesyl diphosphate synthase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 1210595..1211383 | 10450.9 | SNP-level association; inspect population structure before causal interpretation. | ||
| 46 | NC_000962.3_1230778_G_A | NC_000962.3_1230778_G_A | snp | NC_000962.3 | 1230778 | G | A | mazF3 | mRNA interferase MazF3 | Rv1102c | mazF3 | mRNA interferase MazF3 | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(1230660..1230971) | 9884.21 | SNP-level association; inspect population structure before causal interpretation. | |
| 47 | NC_000962.3_1248382_A_G | NC_000962.3_1248382_A_G | snp | NC_000962.3 | 1248382 | A | G | Rv1125 | hypothetical protein | Rv1125 | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 1248082..1249326 | 8436.2 | SNP-level association; inspect population structure before causal interpretation. | ||
| 48 | NC_000962.3_1248936_G_C | NC_000962.3_1248936_G_C | snp | NC_000962.3 | 1248936 | G | C | Rv1125 | hypothetical protein | Rv1125 | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 1248082..1249326 | 9971.67 | SNP-level association; inspect population structure before causal interpretation. | ||
| 49 | NC_000962.3_1250340_A_G | NC_000962.3_1250340_A_G | snp | NC_000962.3 | 1250340 | A | G | ppdK | pyruvate, phosphate dikinase PpdK | Rv1127c | ppdK | pyruvate, phosphate dikinase PpdK | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(1249932..1251404) | 9971.31 | SNP-level association; inspect population structure before causal interpretation. | |
| 50 | NC_000962.3_1254562_A_G | NC_000962.3_1254562_A_G | snp | NC_000962.3 | 1254562 | A | G | prpD | 2-methylcitrate dehydratase | Rv1130 | prpD | 2-methylcitrate dehydratase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 1254555..1256135 | 10439.7 | SNP-level association; inspect population structure before causal interpretation. | |
| 51 | NC_000962.3_1351172_A_G | NC_000962.3_1351172_A_G | snp | NC_000962.3 | 1351172 | A | G | NC_000962.3_1351172_A_G | intergenic_or_unannotated | intergenic_or_unannotated | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 9495.8 | SNP-level association; inspect population structure before causal interpretation. | ||||
| 52 | NC_000962.3_1367484_T_G | NC_000962.3_1367484_T_G | snp | NC_000962.3 | 1367484 | T | G | tatB | Sec-independent protein translocase proteinTatB | Rv1224 | tatB | Sec-independent protein translocase proteinTatB | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 1367463..1367858 | 9492.87 | SNP-level association; inspect population structure before causal interpretation. | |
| 53 | NC_000962.3_1390763_C_T | NC_000962.3_1390763_C_T | snp | NC_000962.3 | 1390763 | C | T | Rv1248c | multifunctional 2-oxoglutarate dehydrogenase E1component /2-oxoglutarate dehydrogenasedihydrolipoyllysine-residue succinyltransferase | Rv1248c | multifunctional 2-oxoglutarate dehydrogenase E1component /2-oxoglutarate dehydrogenasedihydrolipoyllysine-residue succinyltransferase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(1389357..1393052) | 10292.1 | SNP-level association; inspect population structure before causal interpretation. | ||
| 54 | NC_000962.3_1490905_A_G | NC_000962.3_1490905_A_G | snp | NC_000962.3 | 1490905 | A | G | glgB | 1,4-alpha-glucan branching protein | Rv1326c | glgB | 1,4-alpha-glucan branching protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(1490117..1492312) | 9886.08 | SNP-level association; inspect population structure before causal interpretation. | |
| 55 | NC_000962.3_1540141_T_C | NC_000962.3_1540141_T_C | snp | NC_000962.3 | 1540141 | T | C | Rv1367c | hypothetical protein | Rv1367c | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(1539512..1540645) | 8605.35 | SNP-level association; inspect population structure before causal interpretation. | ||
| 56 | NC_000962.3_1544255_C_T | NC_000962.3_1544255_C_T | snp | NC_000962.3 | 1544255 | C | T | Rv1371 | membrane protein | Rv1371 | membrane protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 1543359..1544828 | 10803.8 | SNP-level association; inspect population structure before causal interpretation. | ||
| 57 | NC_000962.3_1546703_C_T | NC_000962.3_1546703_C_T | snp | NC_000962.3 | 1546703 | C | T | Rv1373 | glycolipid sulfotransferase | Rv1373 | glycolipid sulfotransferase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 1546012..1546992 | 11070.8 | SNP-level association; inspect population structure before causal interpretation. | ||
| 58 | NC_000962.3_1608276_A_C | NC_000962.3_1608276_A_C | snp | NC_000962.3 | 1608276 | A | C | Rv1431 | hypothetical protein | Rv1431 | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 1608083..1609852 | 10807.1 | SNP-level association; inspect population structure before causal interpretation. | ||
| 59 | NC_000962.3_1688300_T_C | NC_000962.3_1688300_T_C | snp | NC_000962.3 | 1688300 | T | C | lipL | esterase LipL | Rv1497 | lipL | esterase LipL | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 1687941..1689230 | 9516.64 | SNP-level association; inspect population structure before causal interpretation. | |
| 60 | NC_000962.3_1716472_A_G | NC_000962.3_1716472_A_G | snp | NC_000962.3 | 1716472 | A | G | mmpL12 | transmembrane transport protein MmpL12 | Rv1522c | mmpL12 | transmembrane transport protein MmpL12 | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(1714172..1717612) | 9867.94 | SNP-level association; inspect population structure before causal interpretation. | |
| 61 | NC_000962.3_1849609_T_C | NC_000962.3_1849609_T_C | snp | NC_000962.3 | 1849609 | T | C | lysX | bifunctional lysine--tRNAligase/phosphatidylglycerol lysyltransferase | Rv1640c | lysX | bifunctional lysine--tRNAligase/phosphatidylglycerol lysyltransferase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(1848517..1852035) | 8398.01 | SNP-level association; inspect population structure before causal interpretation. | |
| 62 | NC_000962.3_1859559_C_A | NC_000962.3_1859559_C_A | snp | NC_000962.3 | 1859559 | C | A | pheS | phenylalanine--tRNA ligase subunit alpha | Rv1649 | pheS | phenylalanine--tRNA ligase subunit alpha | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 1858733..1859758 | 9289.76 | SNP-level association; inspect population structure before causal interpretation. | |
| 63 | NC_000962.3_1931718_G_C | NC_000962.3_1931718_G_C | snp | NC_000962.3 | 1931718 | G | C | PPE22 | PPE family protein PPE22 | Rv1705c | PPE22 | PPE family protein PPE22 | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(1931497..1932654) | 7626.39 | SNP-level association; inspect population structure before causal interpretation. | |
| 64 | NC_000962.3_1971725_G_C | NC_000962.3_1971725_G_C | snp | NC_000962.3 | 1971725 | G | C | idi | isopentenyl-diphosphate delta-isomerase | Rv1745c | idi | isopentenyl-diphosphate delta-isomerase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(1971380..1971991) | 9472.86 | SNP-level association; inspect population structure before causal interpretation. | |
| 65 | NC_000962.3_2050822_G_C | NC_000962.3_2050822_G_C | snp | NC_000962.3 | 2050822 | G | C | PPE32 | PPE family protein PPE32 | Rv1808 | PPE32 | PPE family protein PPE32 | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 2049921..2051150 | 7525.18 | SNP-level association; inspect population structure before causal interpretation. | |
| 66 | NC_000962.3_2108890_A_C | NC_000962.3_2108890_A_C | snp | NC_000962.3 | 2108890 | A | C | NC_000962.3_2108890_A_C | intergenic_or_unannotated | intergenic_or_unannotated | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 8217.92 | SNP-level association; inspect population structure before causal interpretation. | ||||
| 67 | NC_000962.3_2122976_C_G | NC_000962.3_2122976_C_G | snp | NC_000962.3 | 2122976 | C | G | lldD2 | L-lactate dehydrogenase | Rv1872c | lldD2 | L-lactate dehydrogenase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(2121907..2123151) | 9511.73 | SNP-level association; inspect population structure before causal interpretation. | |
| 68 | NC_000962.3_2167926_A_G | NC_000962.3_2167926_A_G | snp | NC_000962.3 | 2167926 | A | G | PPE35 | PPE family protein PPE35 | Rv1918c | PPE35 | PPE family protein PPE35 | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(2167649..2170612) | 9935.92 | SNP-level association; inspect population structure before causal interpretation. | |
| 69 | NC_000962.3_2328543_T_C | NC_000962.3_2328543_T_C | snp | NC_000962.3 | 2328543 | T | C | cobM | precorrin-4 C(11)-methyltransferase | Rv2071c | cobM | precorrin-4 C(11)-methyltransferase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(2328222..2328977) | 9450.89 | SNP-level association; inspect population structure before causal interpretation. | |
| 70 | NC_000962.3_2369186_G_C | NC_000962.3_2369186_G_C | snp | NC_000962.3 | 2369186 | G | C | prcA | proteasome subunit alpha | Rv2109c | prcA | proteasome subunit alpha | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(2368983..2369729) | 10550.8 | SNP-level association; inspect population structure before causal interpretation. | |
| 71 | NC_000962.3_2388641_G_A | NC_000962.3_2388641_G_A | snp | NC_000962.3 | 2388641 | G | A | ansP1 | L-asparagine permease | Rv2127 | ansP1 | L-asparagine permease | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 2388616..2390085 | 9535.73 | SNP-level association; inspect population structure before causal interpretation. | |
| 72 | NC_000962.3_2421816_A_G | NC_000962.3_2421816_A_G | snp | NC_000962.3 | 2421816 | A | G | NC_000962.3_2421816_A_G | intergenic_or_unannotated | intergenic_or_unannotated | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 9846.72 | SNP-level association; inspect population structure before causal interpretation. | ||||
| 73 | NC_000962.3_2425471_T_C | NC_000962.3_2425471_T_C | snp | NC_000962.3 | 2425471 | T | C | pbpB | penicillin-binding membrane protein PbpB | Rv2163c | pbpB | penicillin-binding membrane protein PbpB | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(2425048..2427087) | 9773.49 | SNP-level association; inspect population structure before causal interpretation. | |
| 74 | NC_000962.3_2448458_C_T | NC_000962.3_2448458_C_T | snp | NC_000962.3 | 2448458 | C | T | fadD15 | long-chain-fatty-acid--CoA ligase FadD15 | Rv2187 | fadD15 | long-chain-fatty-acid--CoA ligase FadD15 | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 2448160..2449962 | 10113.1 | SNP-level association; inspect population structure before causal interpretation. | |
| 75 | NC_000962.3_2470591_A_C | NC_000962.3_2470591_A_C | snp | NC_000962.3 | 2470591 | A | C | NC_000962.3_2470591_A_C | intergenic_or_unannotated | intergenic_or_unannotated | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 10138.6 | SNP-level association; inspect population structure before causal interpretation. | ||||
| 76 | NC_000962.3_2619271_T_C | NC_000962.3_2619271_T_C | snp | NC_000962.3 | 2619271 | T | C | NC_000962.3_2619271_T_C | intergenic_or_unannotated | intergenic_or_unannotated | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 9288.42 | SNP-level association; inspect population structure before causal interpretation. | ||||
| 77 | NC_000962.3_2723506_T_C | NC_000962.3_2723506_T_C | snp | NC_000962.3 | 2723506 | T | C | Rv2426c | hypothetical protein | Rv2426c | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(2723308..2724183) | 9870.52 | SNP-level association; inspect population structure before causal interpretation. | ||
| 78 | NC_000962.3_2740693_T_C | NC_000962.3_2740693_T_C | snp | NC_000962.3 | 2740693 | T | C | NC_000962.3_2740693_T_C | intergenic_or_unannotated | intergenic_or_unannotated | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 8109 | SNP-level association; inspect population structure before causal interpretation. | ||||
| 79 | NC_000962.3_2791098_C_T | NC_000962.3_2791098_C_T | snp | NC_000962.3 | 2791098 | C | T | Rv2484c | diacyglycerol O-acyltransferase | Rv2484c | diacyglycerol O-acyltransferase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(2791019..2792494) | 9829.25 | SNP-level association; inspect population structure before causal interpretation. | ||
| 80 | NC_000962.3_2807486_C_A | NC_000962.3_2807486_C_A | snp | NC_000962.3 | 2807486 | C | A | Rv2492 | hypothetical protein | Rv2492 | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 2807278..2808030 | 12836.8 | SNP-level association; inspect population structure before causal interpretation. | ||
| 81 | NC_000962.3_2825466_G_A | NC_000962.3_2825466_G_A | snp | NC_000962.3 | 2825466 | G | A | Rv2509 | short-chain type dehydrogenase/reductase | Rv2509 | short-chain type dehydrogenase/reductase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 2824678..2825484 | 10198.3 | SNP-level association; inspect population structure before causal interpretation. | ||
| 82 | NC_000962.3_2841022_A_G | NC_000962.3_2841022_A_G | snp | NC_000962.3 | 2841022 | A | G | fas | fatty acid synthase | Rv2524c | fas | fatty acid synthase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(2840123..2849332) | 7982.93 | SNP-level association; inspect population structure before causal interpretation. | |
| 83 | NC_000962.3_2847281_A_G | NC_000962.3_2847281_A_G | snp | NC_000962.3 | 2847281 | A | G | fas | fatty acid synthase | Rv2524c | fas | fatty acid synthase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(2840123..2849332) | 10044.1 | SNP-level association; inspect population structure before causal interpretation. | |
| 84 | NC_000962.3_2886570_A_G | NC_000962.3_2886570_A_G | snp | NC_000962.3 | 2886570 | A | G | Rv2566 | hypothetical protein | Rv2566 | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 2886373..2889795 | 9226.08 | SNP-level association; inspect population structure before causal interpretation. | ||
| 85 | NC_000962.3_2925962_T_C | NC_000962.3_2925962_T_C | snp | NC_000962.3 | 2925962 | T | C | vapC40 | ribonuclease VapC40 | Rv2596 | vapC40 | ribonuclease VapC40 | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 2925734..2926138 | 9247.44 | SNP-level association; inspect population structure before causal interpretation. | |
| 86 | NC_000962.3_3003115_C_G | NC_000962.3_3003115_C_G | snp | NC_000962.3 | 3003115 | C | G | arsB1 | arsenic-transport integral membrane proteinArsB | Rv2685 | arsB1 | arsenic-transport integral membrane proteinArsB | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 3001983..3003269 | 10659.1 | SNP-level association; inspect population structure before causal interpretation. | |
| 87 | NC_000962.3_3010420_A_G | NC_000962.3_3010420_A_G | snp | NC_000962.3 | 3010420 | A | G | ceoC | TRK system potassium uptake protein CeoC | Rv2692 | ceoC | TRK system potassium uptake protein CeoC | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 3010024..3010686 | 8991.71 | SNP-level association; inspect population structure before causal interpretation. | |
| 88 | NC_000962.3_3027798_T_C | NC_000962.3_3027798_T_C | snp | NC_000962.3 | 3027798 | T | C | Rv2714 | hypothetical protein | Rv2714 | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 3027065..3028039 | 9329.25 | SNP-level association; inspect population structure before causal interpretation. | ||
| 89 | NC_000962.3_3031168_A_G | NC_000962.3_3031168_A_G | snp | NC_000962.3 | 3031168 | A | G | Rv2719c | membrane protein | Rv2719c | membrane protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(3031040..3031537) | 9659.33 | SNP-level association; inspect population structure before causal interpretation. | ||
| 90 | NC_000962.3_3104189_A_G | NC_000962.3_3104189_A_G | snp | NC_000962.3 | 3104189 | A | G | Rv2795c | hypothetical protein | Rv2795c | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(3103937..3104911) | 9364.51 | SNP-level association; inspect population structure before causal interpretation. | ||
| 91 | NC_000962.3_3112877_G_A | NC_000962.3_3112877_G_A | snp | NC_000962.3 | 3112877 | G | A | Rv2804c | hypothetical protein | Rv2804c | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(3112465..3113094) | 9698.65 | SNP-level association; inspect population structure before causal interpretation. | ||
| 92 | NC_000962.3_3174496_A_G | NC_000962.3_3174496_A_G | snp | NC_000962.3 | 3174496 | A | G | Rv2862c | hypothetical protein | Rv2862c | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(3174059..3174643) | 9262.41 | SNP-level association; inspect population structure before causal interpretation. | ||
| 93 | NC_000962.3_3189242_A_G | NC_000962.3_3189242_A_G | snp | NC_000962.3 | 3189242 | A | G | mpt53 | soluble secreted antigen Mpt53 | Rv2878c | mpt53 | soluble secreted antigen Mpt53 | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(3188876..3189397) | 10715.4 | SNP-level association; inspect population structure before causal interpretation. | |
| 94 | NC_000962.3_3314412_A_G | NC_000962.3_3314412_A_G | snp | NC_000962.3 | 3314412 | A | G | Rv2962c | PGL/p-HBAD biosynthesis rhamnosyltransferase | Rv2962c | PGL/p-HBAD biosynthesis rhamnosyltransferase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(3313773..3315122) | 10373.5 | SNP-level association; inspect population structure before causal interpretation. | ||
| 95 | NC_000962.3_3326554_A_C | NC_000962.3_3326554_A_C | snp | NC_000962.3 | 3326554 | A | C | Rv2971 | oxidoreductase | Rv2971 | oxidoreductase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 3326101..3326949 | 11532.8 | SNP-level association; inspect population structure before causal interpretation. | ||
| 96 | NC_000962.3_3335708_G_C | NC_000962.3_3335708_G_C | snp | NC_000962.3 | 3335708 | G | C | Rv2979c | resolvase | Rv2979c | resolvase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(3335164..3335748) | 10012.4 | SNP-level association; inspect population structure before causal interpretation. | ||
| 97 | NC_000962.3_3420825_A_G | NC_000962.3_3420825_A_G | snp | NC_000962.3 | 3420825 | A | G | cyp136 | cytochrome P450 Cyp136 | Rv3059 | cyp136 | cytochrome P450 Cyp136 | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 3419492..3420970 | 10918.9 | SNP-level association; inspect population structure before causal interpretation. | |
| 98 | NC_000962.3_3454263_C_G | NC_000962.3_3454263_C_G | snp | NC_000962.3 | 3454263 | C | G | Rv3087 | diacyglycerol O-acyltransferase | Rv3087 | diacyglycerol O-acyltransferase | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | 3452925..3454343 | 10102.1 | SNP-level association; inspect population structure before causal interpretation. | ||
| 99 | NC_000962.3_3467465_C_G | NC_000962.3_3467465_C_G | snp | NC_000962.3 | 3467465 | C | G | Rv3098c | hypothetical protein | Rv3098c | hypothetical protein | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(3467210..3467662) | 9469.12 | SNP-level association; inspect population structure before causal interpretation. | ||
| 100 | NC_000962.3_3510120_T_G | NC_000962.3_3510120_T_G | snp | NC_000962.3 | 3510120 | T | G | PPE52 | PPE family protein PPE52 | Rv3144c | PPE52 | PPE family protein PPE52 | 50 | 50 | 1.0000 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 9.55 | 10201 | 198.5-5.242e+05 | 198.519 | 524185 | 4.54e-18 | 17.3429 | reference_GenBank_coordinate_overlap | complement(3510088..3511317) | 10017 | SNP-level association; inspect population structure before causal interpretation. |
Showing 100 of 100 rows.
metric value snp_gwas_status prioritized pyseer_snp_rows 17248 ranked_snp_features 17248 significant_snp_features 1798 alpha 0.05
Recombination intervals: 0. Output files: MTB_rpoB_763031_44v44_marker_validation_SNP_gubbins_summary.tsv, MTB_rpoB_763031_44v44_marker_validation_SNP_gubbins.filtered_polymorphic_sites.fasta, MTB_rpoB_763031_44v44_marker_validation_SNP_gubbins.recombination_predictions.gff, and MTB_rpoB_763031_44v44_marker_validation_SNP_gubbins.log.
metric value gubbins_status not_run recommendation Optional. Enable for recombining bacteria or strong lineage/recombination concerns; usually not required as a default for MTBC/clonal analyses. usage_note Gubbins not requested. Primary SNP GWAS used the unfiltered Snippy/core VCF when SNP GWAS was enabled.
50S ribosomal protein L23
cytochrome C-type biogenesis protein CcdA
cytochrome P450 Cyp144
HTH-type transcriptional regulator NmtR
transmembrane protein
| rank | feature id | feature type | display name | display label | gene name | product | reference locus tag | reference gene | reference product | annotation confidence | reference identity | reference coverage | interpretation note | annotation evidence | case (rpoB 763031 T C present) present | case (rpoB 763031 T C present) total | case (rpoB 763031 T C present) frequency | control (rpoB 763031 T C absent) present | control (rpoB 763031 T C absent) total | control (rpoB 763031 T C absent) frequency | enriched in | beta | odds ratio | odds ratio ci95 | odds ratio ci95 lower | odds ratio ci95 upper | pyseer pvalue | q value | priority score | annotation source | reference match type | reference location | annotation note | cluster member ids | notes | display product |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | group_2286 | gene_presence_absence | rplW | group_2286 | Rv0703 | none confidence | rplW | 50S ribosomal protein L23 | Rv0703 | rplW | 50S ribosomal protein L23 | none | 21.83 | 1.93 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=21.83; coverage=1.93 | 1 | 50 | 0.0200 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -7.78 | 0.00030003 | 1.193e-05-0.007544 | 1.19329e-05 | 0.00754369 | 3.56e-16 | 30.1512 | Panaroo/Bakta+GenBank | nucleotide_similarity | 802133..802435 | matched_representative_sequence=group_2286 | AEDLOG_01250;AFKOAF_02797;APAKNA_00381;BDILPO_00329;BDMCKA_00770;BGEAED_00081;BHJHEC_01439;BKLOHC_00975;BPLIPK_01269;CBPCJH_00995;DOFGLF_01828;DPLIOB_00501;EEGMED_02335;EEMIBL_01291;FGOACM_00119;FLEJOH_01885;FNLDAG_02828;FOMADB_00225;GAGFCG_00499;GKEIOM_01002;GKLDEJ_00380;HBIPEG_01813;HFAJAL_00718;HFPBEP_02167;HIHJDO_03875;HLEDKO_00971;IJGDKF_00488;ILFCIO_01192;IOJEPD_00265;IPDLAB_00716 | 50S ribosomal protein L23 | ||
| 2 | group_3150 | gene_presence_absence | ccdA | group_3150 | Rv0527 | none confidence | ccdA | cytochrome C-type biogenesis protein CcdA | Rv0527 | ccdA | cytochrome C-type biogenesis protein CcdA | none | 36.55 | 2.47 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=36.55; coverage=2.47 | 49 | 50 | 0.9800 | 1 | 50 | 0.0200 | cases (rpoB 763031 T C present) | 8.78 | 1089 | 109.5-1.083e+04 | 109.483 | 10832 | 3.46e-16 | 28.5497 | Panaroo/Bakta+GenBank | nucleotide_similarity | 617493..618272 | matched_representative_sequence=group_3150 | AEMPHK_02800;AEMPHK_02801;AFNKCG_02062;AFNKCG_02063;ANMCAC_03049;ANMCAC_03050;BHJHEC_04034;BHJHEC_04035;BPEJMN_02687;BPEJMN_02688;CIMEKD_02693;CIMEKD_02694;CKHCDK_01640;DBCCLE_02628;DBCCLE_02629;DJMHJN_03235;DJMHJN_03236;DNOEHN_01662;DNOEHN_01663;EBKMEK_02740;EBKMEK_02741;EOJHMN_01713;EOJHMN_01714;EPBFME_02959;EPBFME_02960;FDDMPP_03885;FDDMPP_03886;FNACPH_03144;FNACPH_03145;GNKHBM_02961 | cytochrome C-type biogenesis protein CcdA | ||
| 3 | group_2789 | gene_presence_absence | cyp144 | group_2789 | Rv1777 | none confidence | cyp144 | cytochrome P450 Cyp144 | Rv1777 | cyp144 | cytochrome P450 Cyp144 | none | 18.31 | 6.09 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=18.31; coverage=6.09 | 49 | 50 | 0.9800 | 1 | 50 | 0.0200 | cases (rpoB 763031 T C present) | 8.78 | 1089 | 109.5-1.083e+04 | 109.483 | 10832 | 3.46e-16 | 28.5497 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2010656..2011960 | matched_representative_sequence=group_2789 | AEMPHK_02802;AFNKCG_02064;ANMCAC_03051;BHJHEC_04033;BPEJMN_02689;CIMEKD_02695;CKHCDK_01642;DBCCLE_02627;DJMHJN_03234;DNOEHN_01664;EBKMEK_02739;EOJHMN_01712;EPBFME_02961;FDDMPP_03887;FNACPH_03146;GNKHBM_02963;HEJICF_02747;HIHJDO_00196;HLIGOK_02329;HNJHNP_02577;ICLPCH_01675;IDADDB_02773;IEDNOI_02333;IJKJHL_01495;ILDPAE_03117;IMGGMF_01607;INBOBH_02518;JGDOPI_03074;JGFCNM_03002;JIEBBG_02335 | cytochrome P450 Cyp144 | ||
| 4 | group_2968 | gene_presence_absence | nmtR | group_2968 | Rv3744 | none confidence | nmtR | hypothetical protein;PknH-like extracellular domain-containing protein | Rv3744 | nmtR | HTH-type transcriptional regulator NmtR | none | 30.27 | 2.28 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=30.27; coverage=2.28 | 48 | 50 | 0.9600 | 1 | 50 | 0.0200 | cases (rpoB 763031 T C present) | 7.8 | 640.2 | 81.38-5036 | 81.3801 | 5036.32 | 6.25e-15 | 26.5265 | Panaroo/Bakta+GenBank | nucleotide_similarity | 4195440..4195802 | matched_representative_sequence=group_2968 | AEMPHK_02798;AFNKCG_02060;ANMCAC_03047;BHJHEC_04037;BPEJMN_02685;CIMEKD_02691;CKHCDK_01638;DBCCLE_02631;DJMHJN_03238;DNOEHN_01660;EBKMEK_02743;EOJHMN_01716;EPBFME_02957;FDDMPP_03883;FNACPH_03142;GNKHBM_02959;HEJICF_02743;HIHJDO_00193;HLIGOK_02333;HNJHNP_02573;ICLPCH_01672;IDADDB_02769;IEDNOI_02337;IJKJHL_01491;ILDPAE_03121;IMGGMF_01603;INBOBH_02522;JGDOPI_03078;JGFCNM_03006;KBONAM_02586 | HTH-type transcriptional regulator NmtR | ||
| 5 | group_1329 | gene_presence_absence | group_1329 | group_1329 | Rv2620c | none confidence | group_1329 | PknH-like extracellular domain-containing protein | Rv2620c | transmembrane protein | none | 40.71 | 1.86 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=40.71; coverage=1.86 | 48 | 50 | 0.9600 | 1 | 50 | 0.0200 | cases (rpoB 763031 T C present) | 7.8 | 640.2 | 81.38-5036 | 81.3801 | 5036.32 | 6.25e-15 | 26.5265 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(2947462..2947887) | matched_representative_sequence=group_1329 | AEMPHK_02799;AFNKCG_02061;ANMCAC_03048;BHJHEC_04036;BPEJMN_02686;CIMEKD_02692;CKHCDK_01639;DBCCLE_02630;DJMHJN_03237;DNOEHN_01661;EBKMEK_02742;EOJHMN_01715;EPBFME_02958;FDDMPP_03884;FNACPH_03143;GNKHBM_02960;HEJICF_02744;HIHJDO_00194;HLIGOK_02332;HNJHNP_02574;ICLPCH_01673;IDADDB_02770;IEDNOI_02336;IJKJHL_01492;ILDPAE_03120;IMGGMF_01604;INBOBH_02521;JGDOPI_03077;JGFCNM_03005;KBONAM_02587 | transmembrane protein | |||
| 6 | group_2915 | gene_presence_absence | dnaK | group_2915 | Rv0350 | none confidence | dnaK | Translation elongation factor EFTu-like domain-containing protein | Rv0350 | dnaK | chaperone protein DnaK | none | 11.36 | 5.56 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=11.36; coverage=5.56 | 46 | 50 | 0.9200 | 1 | 50 | 0.0200 | cases (rpoB 763031 T C present) | 6.26 | 341 | 51.48-2259 | 51.4763 | 2258.92 | 1.12e-11 | 22.3644 | Panaroo/Bakta+GenBank | nucleotide_similarity | 419835..421712 | matched_representative_sequence=group_2915 | AEMPHK_02797;AFNKCG_02059;ANMCAC_03046;BHJHEC_04038;BPEJMN_02684;CKHCDK_01637;DBCCLE_02632;DJMHJN_03239;DNOEHN_01659;EBKMEK_02744;EOJHMN_01717;EPBFME_02956;FDDMPP_03882;FNACPH_03141;GNKHBM_02958;HEJICF_02742;HIHJDO_00192;HLIGOK_02334;HNJHNP_02572;ICLPCH_01671;IDADDB_02768;IEDNOI_02338;IJKJHL_01490;ILDPAE_03122;IMGGMF_01602;INBOBH_02523;JGDOPI_03079;JGFCNM_03007;KBONAM_02585;LABCDH_03046 | chaperone protein DnaK | ||
| 7 | group_161 | gene_presence_absence | vapC13 | group_161 | Rv1838c | high confidence | vapC13 | ribonuclease VapC13 | Rv1838c | vapC13 | ribonuclease VapC13 | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 46 | 50 | 0.9200 | 1 | 50 | 0.0200 | cases (rpoB 763031 T C present) | 6.26 | 341 | 51.48-2259 | 51.4763 | 2258.92 | 1.12e-11 | 22.3644 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(2087257..2087652) | matched_representative_sequence=group_1612 | 17_refound_723_pseudo;AEMPHK_02796;AFNKCG_02058;ANMCAC_03045;BHJHEC_04039;BPEJMN_02683;CKHCDK_01636;DBCCLE_02633;DJMHJN_03240;DNOEHN_01658;EBKMEK_02745;EOJHMN_01718;EPBFME_02955;FDDMPP_03881;FNACPH_03140;GNKHBM_02957;HEJICF_02741;HIHJDO_00191;HLIGOK_02335;HNJHNP_02571;ICLPCH_01670;IDADDB_02767;IEDNOI_02339;IJKJHL_01489;ILDPAE_03123;IMGGMF_01601;INBOBH_02524;JGDOPI_03080;JGFCNM_03008;KBONAM_02584 | ribonuclease VapC13 | ||
| 8 | group_2755 | gene_presence_absence | Rv3785-like (group_2755) | group_2755 | Rv3785 | low confidence | group_2755 | hypothetical protein | Rv3785 | hypothetical protein | low | 72.82 | 88.62 | Low-confidence locus-level GenBank rescue. | identity=72.82; coverage=88.62 | 44 | 50 | 0.8800 | 3 | 50 | 0.0600 | cases (rpoB 763031 T C present) | 5.41 | 92.9121 | 23.79-362.8 | 23.7925 | 362.831 | 3.29e-11 | 20.0206 | Panaroo/Bakta+GenBank | nucleotide_similarity | 4231320..4232393 | matched_representative_sequence=group_2755 | AEMPHK_01496;AFNKCG_02801;ANMCAC_02133;BPEJMN_02072;CIMEKD_00431;DBCCLE_02436;DJMHJN_01642;DNOEHN_01387;EBKMEK_01641;EOJHMN_00730;EPBFME_01975;FDDMPP_02356;FNACPH_02067;GKLDEJ_02727;GNKHBM_01779;HEJICF_00699;HFAJAL_00786;HLIGOK_01549;HNJHNP_01531;IDADDB_01398;IEDNOI_01429;IJKJHL_01789;ILDPAE_01809;IMGGMF_01300;INBOBH_01400;JFNAAB_02666;JGDOPI_01970;JGFCNM_02208;JIEBBG_02313;KBONAM_00870 | hypothetical protein | |||
| 9 | group_2940 | gene_presence_absence | Rv0072 (group_2940) | group_2940 | Rv0072 | high confidence | group_2940 | hypothetical protein;Uncharacterized ABC transporter permease Rv0072 | Rv0072 | glutamine ABC transporter permease | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 14 | 50 | 0.2800 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -7.21 | 0.00393327 | 0.0002272-0.06808 | 0.00022724 | 0.0680806 | 9.95e-08 | 17.9922 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 80624..81673 | matched_representative_sequence=group_2940 | AEDLOG_00549;AFKOAF_01003;AFNKCG_04006;APAKNA_00137;BDILPO_03208;BDILPO_03943;BDMCKA_01131;BGEAED_00406;BHJHEC_00672;BKLOHC_00643;BPLIPK_00383;CBPCJH_00606;CKHCDK_02351;DOFGLF_03651;DPLIOB_00705;EEGMED_00127;EEMIBL_01538;FDDMPP_03192;FGOACM_00552;FLEJOH_00554;FNLDAG_00651;FOMADB_00775;GAGFCG_00966;GKEIOM_02346;GKLDEJ_02611;HBIPEG_01035;HEJICF_02135;HFAJAL_00212;HFPBEP_02094;HIHJDO_03987 | glutamine ABC transporter permease | |||
| 10 | group_1076 | gene_presence_absence | Rv0073 (group_1076) | group_1076 | Rv0073 | high confidence | group_1076 | ABC transporter domain-containing protein;hypothetical protein;Uncharacterized ABC transporter ATP-binding protein Rv0073 | Rv0073 | glutamine ABC transporter ATP-binding protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 14 | 50 | 0.2800 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -7.21 | 0.00393327 | 0.0002272-0.06808 | 0.00022724 | 0.0680806 | 9.95e-08 | 17.9922 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 81676..82668 | matched_representative_sequence=group_1076 | AEDLOG_00550;AFKOAF_01004;AFNKCG_04007;APAKNA_00136;BDILPO_03942;BDMCKA_01132;BGEAED_00405;BHJHEC_00671;BKLOHC_00644;BPLIPK_00382;CBPCJH_00605;CKHCDK_02350;DOFGLF_03652;DPLIOB_00706;EEGMED_00126;EEMIBL_01539;FDDMPP_03193;FGOACM_00551;FLEJOH_00555;FNLDAG_00652;FOMADB_00774;GAGFCG_00967;GKEIOM_02344;GKEIOM_02345;GKLDEJ_02612;HBIPEG_01034;HEJICF_02136;HFAJAL_00213;HFPBEP_02093;HIHJDO_03988 | glutamine ABC transporter ATP-binding protein | |||
| 11 | group_2793 | gene_presence_absence | vapB17 | group_2793 | Rv2526 | high confidence | vapB17 | hypothetical protein;Putative antitoxin VapB17 | Rv2526 | vapB17 | antitoxin VapB17 | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 15 | 50 | 0.3000 | 48 | 50 | 0.9600 | controls (rpoB 763031 T C absent) | -8.36 | 0.0225062 | 0.005526-0.09166 | 0.00552644 | 0.0916554 | 4.45e-10 | 17.8252 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 2851091..2851318 | matched_representative_sequence=13_refound_614 | 0_refound_139_pseudo;13_refound_614;3_refound_310_pseudo;41_refound_1351;44_refound_1462_pseudo;95_refound_2398_pseudo;AEDLOG_02135;AFKOAF_02067;AFNKCG_01693;APAKNA_01180;BDILPO_02295;BDMCKA_03456;BGEAED_00726;BHJHEC_01984;BPLIPK_02171;CBPCJH_01673;CKHCDK_02633;DOFGLF_01063;DPLIOB_02775;EEGMED_02427;EEMIBL_02636;FDDMPP_01524;FGOACM_02375;FLEJOH_02998;FOMADB_02868;GAGFCG_02739;GKEIOM_02775;GKLDEJ_01940;HBIPEG_02183;HEJICF_02077 | antitoxin VapB17 | ||
| 12 | group_2962 | gene_presence_absence | PE_PGRS49-like (group_2962) | group_2962 | Rv3344c | low confidence | PE_PGRS49 | PE-PGRS family protein PE_PGRS49 | Rv3344c | PE_PGRS49 | PE-PGRS family protein PE_PGRS49 | low | 100.00 | 50.00 | Low-confidence GenBank rescue; treat as tentative and keep the Panaroo cluster ID. | identity=100.00; coverage=50.00 | 3 | 50 | 0.0600 | 29 | 50 | 0.5800 | controls (rpoB 763031 T C absent) | -4.39 | 0.0537021 | 0.01586-0.1818 | 0.0158611 | 0.181823 | 2.24e-09 | 15.8686 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(3736984..3738000) | matched_representative_sequence=group_2962 | AFKOAF_04101;APAKNA_04083;BDILPO_03516;BGEAED_03867;BGEAED_03868;CBPCJH_03768;CBPCJH_03769;DOFGLF_03839;EEGMED_03522;EEGMED_03523;EEMIBL_03822;EEMIBL_03823;FGOACM_03029;FLEJOH_04049;GAGFCG_03889;GKLDEJ_03872;HBIPEG_03846;HBIPEG_03847;HFAJAL_03963;HIHJDO_01905;IJGDKF_03790;IJGDKF_03791;ILFCIO_04100;IOJEPD_04096;IPDLAB_03880;JFNAAB_03083;KOLHLA_03646;KOLHLA_03647;LNDNPG_04035;MHDACH_03535 | PE-PGRS family protein PE_PGRS49 | ||
| 13 | group_3104 | gene_presence_absence | Rv2817c (group_3104) | group_3104 | Rv2817c | high confidence | group_3104 | hypothetical protein;CRISPR-associated endonuclease Cas1 | Rv2817c | CRISPR-associated endonuclease Cas1 | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 16 | 50 | 0.3200 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -6.53 | 0.00473526 | 0.0002748-0.08159 | 0.000274825 | 0.0815887 | 8.27e-06 | 15.8048 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(3123967..3124983) | matched_representative_sequence=group_3104 | AEDLOG_03397;AFKOAF_03866;AFNKCG_03654;APAKNA_01917;BDILPO_02936;BDMCKA_04006;BGEAED_01074;BHJHEC_03982;BKLOHC_01955;BPLIPK_03786;CBPCJH_00768;CKHCDK_03908;DBCCLE_04047;DOFGLF_04000;DPLIOB_03469;EEGMED_03865;EEMIBL_02759;FDDMPP_04032;FGOACM_03625;FLEJOH_00580;FNLDAG_03547;FOMADB_03903;GAGFCG_01313;GKEIOM_01271;GKLDEJ_03610;HBIPEG_00829;HEJICF_03824;HFAJAL_00244;HFPBEP_03209;HIHJDO_02730 | CRISPR-associated endonuclease Cas1 | |||
| 14 | group_2919 | gene_presence_absence | Rv2818c (group_2919) | group_2919 | Rv2818c | high confidence | group_2919 | hypothetical protein;CRISPR system endoribonuclease Csm6 | Rv2818c | CRISPR-associated protein Csm6 | high | 100.00 | 92.07 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=92.07 | 16 | 50 | 0.3200 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -6.53 | 0.00473526 | 0.0002748-0.08159 | 0.000274825 | 0.0815887 | 8.27e-06 | 15.8048 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(3124996..3126144) | matched_representative_sequence=group_2919 | AEDLOG_03396;AFKOAF_03867;AFNKCG_03655;APAKNA_01916;BDILPO_02937;BDMCKA_04005;BGEAED_01075;BHJHEC_03983;BKLOHC_01954;BPLIPK_03785;CBPCJH_00769;CKHCDK_03909;DBCCLE_03584;DOFGLF_03999;DPLIOB_03470;EEGMED_03866;EEMIBL_02758;FDDMPP_04031;FGOACM_03624;FLEJOH_00581;FNLDAG_03548;FOMADB_03902;GAGFCG_01312;GKEIOM_01272;GKLDEJ_03611;HBIPEG_00828;HEJICF_03825;HFAJAL_00245;HFPBEP_03210;HIHJDO_02731 | CRISPR-associated protein Csm6 | |||
| 15 | group_1498 | gene_presence_absence | lppA | group_1498 | Rv2543 | high confidence | lppA | lipoprotein LppA | Rv2543 | lppA | lipoprotein LppA | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 16 | 50 | 0.3200 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -6.53 | 0.00473526 | 0.0002748-0.08159 | 0.000274825 | 0.0815887 | 8.27e-06 | 15.8048 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 2866468..2867127 | matched_representative_sequence=group_1498 | 50_refound_1544_pseudo;AEDLOG_02118;AFKOAF_02050;AFNKCG_01711;APAKNA_01197;BDILPO_02277;BDMCKA_02893;BGEAED_00709;BHJHEC_01967;BKLOHC_03083;BPLIPK_02154;CBPCJH_01690;CKHCDK_02650;DBCCLE_01505;DOFGLF_01080;DPLIOB_02758;EEGMED_02444;EEMIBL_02619;FDDMPP_01507;FGOACM_02358;FLEJOH_02981;FNLDAG_03133;FOMADB_01728;GAGFCG_02756;GKEIOM_02758;GKLDEJ_01957;HBIPEG_02166;HEJICF_02094;HFAJAL_01119;HFPBEP_03679 | lipoprotein LppA | ||
| 16 | group_915 | gene_presence_absence | Rv2819c (group_915) | group_915 | Rv2819c | high confidence | group_915 | hypothetical protein;CRISPR system Cms protein Csm5 | Rv2819c | CRISPR type III-associated RAMP protein Csm5 | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 16 | 50 | 0.3200 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -6.53 | 0.00473526 | 0.0002748-0.08159 | 0.000274825 | 0.0815887 | 8.27e-06 | 15.8048 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(3126240..3127367) | matched_representative_sequence=group_915 | AEDLOG_03395;AFKOAF_03868;AFNKCG_03656;APAKNA_01915;BDILPO_02938;BDMCKA_04004;BGEAED_01076;BHJHEC_03984;BKLOHC_01953;BPLIPK_03784;CBPCJH_00770;CKHCDK_03910;DBCCLE_03585;DOFGLF_03998;DPLIOB_03471;EEGMED_03867;EEMIBL_02757;FDDMPP_04030;FGOACM_03623;FLEJOH_00582;FNLDAG_03549;FOMADB_03901;GAGFCG_01311;GKEIOM_01273;GKLDEJ_03612;HBIPEG_00827;HEJICF_03826;HFAJAL_00246;HFPBEP_03211;HIHJDO_02732 | CRISPR type III-associated RAMP protein Csm5 | |||
| 17 | group_3239 | gene_presence_absence | PPE67 | group_3239 | Rv3739c | high confidence | PPE67 | PPE family protein PPE67 | Rv3739c | PPE67 | PPE family protein PPE67 | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 36 | 50 | 0.7200 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -12.1 | 0.0249232 | 0.00144-0.4314 | 0.00143991 | 0.431393 | 1.48e-07 | 15.1561 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(4190284..4190517) | matched_representative_sequence=group_3239 | 81_refound_2035_pseudo;AEDLOG_01234;AEMPHK_01548;AFKOAF_01479;ANMCAC_02185;APAKNA_00365;BDILPO_00313;BDMCKA_00754;BGEAED_00065;BHJHEC_01455;BKLOHC_02036;BPEJMN_02124;BPLIPK_01285;CBPCJH_00979;CIMEKD_00483;DBCCLE_02384;DJMHJN_01694;DNOEHN_01335;DOFGLF_01844;DPLIOB_00485;EBKMEK_01589;EEGMED_02351;EEMIBL_01307;EOJHMN_00678;EPBFME_02028;FGOACM_00135;FLEJOH_01901;FNACPH_02119;FNLDAG_00495;FOMADB_00241 | PPE family protein PPE67 | ||
| 18 | group_897 | gene_presence_absence | mpt83 | group_897 | Rv2873 | none confidence | mpt83 | cell surface lipoprotein | Rv2873 | mpt83 | cell surface lipoprotein | none | 16.09 | 5.44 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=16.09; coverage=5.44 | 5 | 50 | 0.1000 | 43 | 50 | 0.8600 | controls (rpoB 763031 T C absent) | -3.3 | 0.0208412 | 0.006428-0.06757 | 0.00642849 | 0.0675674 | 5.54e-07 | 14.8409 | Panaroo/Bakta+GenBank | nucleotide_similarity | 3183905..3184567 | matched_representative_sequence=group_897 | 20_refound_835_pseudo;AEDLOG_01658;AFKOAF_01016;APAKNA_01389;BDILPO_02737;BGEAED_03378;BHJHEC_00399;BKLOHC_00365;BPLIPK_00110;CBPCJH_00913;CKHCDK_01352;DOFGLF_01788;EEGMED_01902;EEMIBL_02271;FGOACM_01579;FLEJOH_03462;FNLDAG_00136;FOMADB_00373;GAGFCG_03079;GKEIOM_00883;GKLDEJ_00243;HEJICF_01674;HFAJAL_00389;HFPBEP_00151;HLEDKO_00282;ICLPCH_02639;IJGDKF_00069;ILFCIO_00808;IOJEPD_03535;JEBLOM_00083 | cell surface lipoprotein | ||
| 19 | group_1075 | gene_presence_absence | Rv0071 (group_1075) | group_1075 | Rv0071 | high confidence | group_1075 | maturase | Rv0071 | maturase | high | 97.52 | 92.61 | High-confidence locus-level GenBank rescue. | identity=97.52; coverage=92.61 | 14 | 50 | 0.2800 | 49 | 50 | 0.9800 | controls (rpoB 763031 T C absent) | -5.65 | 0.0120382 | 0.002124-0.06822 | 0.00212437 | 0.0682168 | 2e-05 | 14.0752 | Panaroo/Bakta+GenBank | nucleotide_similarity | 79486..80193 | matched_representative_sequence=group_1075 | AEDLOG_00548;AFKOAF_01002;AFNKCG_03799;APAKNA_00138;BDILPO_03207;BDMCKA_01130;BGEAED_00407;BHJHEC_00673;BKLOHC_00642;BPLIPK_00384;CBPCJH_00607;CKHCDK_02352;DOFGLF_00812;DPLIOB_00704;EEGMED_00128;EEMIBL_01537;FDDMPP_03191;FGOACM_00553;FLEJOH_00553;FNLDAG_00650;FOMADB_00776;GAGFCG_00965;GKEIOM_02347;GKLDEJ_02610;HBIPEG_01036;HEJICF_02134;HFAJAL_00211;HFPBEP_02095;HIHJDO_03986;HLEDKO_00415 | maturase | |||
| 20 | group_2489 | gene_presence_absence | PPE46 | group_2489 | Rv3018c | none confidence | PPE46 | hypothetical protein;Uncharacterized PPE family protein PPE66 | Rv3018c | PPE46 | PPE family protein PPE46 | none | 60.60 | 1.95 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=60.60; coverage=1.95 | 39 | 50 | 0.7800 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -4.93 | 0.0340077 | 0.001944-0.595 | 0.00194385 | 0.594968 | 5.37e-06 | 13.1480 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(3376939..3378243) | matched_representative_sequence=group_2489 | AEDLOG_01235;AEMPHK_01549;AFKOAF_01480;ANMCAC_02186;APAKNA_00366;BDILPO_00314;BDMCKA_00755;BGEAED_00066;BHJHEC_01454;BKLOHC_02035;BPEJMN_02125;BPLIPK_01284;CBPCJH_00980;CIMEKD_00484;DJMHJN_01695;DNOEHN_01334;DOFGLF_01843;DPLIOB_00486;EBKMEK_01588;EEGMED_02350;EEMIBL_01306;EOJHMN_00677;EPBFME_02029;FGOACM_00134;FLEJOH_01900;FNACPH_02120;FNLDAG_00496;FOMADB_00240;GAGFCG_00484;GKEIOM_00988 | PPE family protein PPE46 | ||
| 21 | group_2067 | gene_presence_absence | Rv2816c (group_2067) | group_2067 | Rv2816c | high confidence | group_2067 | CRISPR-associated endoribonuclease Cas2 | Rv2816c | CRISPR-associated endoribonuclease Cas2 | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 16 | 50 | 0.3200 | 49 | 50 | 0.9800 | controls (rpoB 763031 T C absent) | -5.37 | 0.0144928 | 0.002577-0.08151 | 0.00257682 | 0.0815113 | 0.000476 | 12.4309 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(3123625..3123966) | matched_representative_sequence=group_2067 | AEDLOG_03398;AFKOAF_03865;AFNKCG_03653;APAKNA_01918;BDILPO_02935;BDMCKA_04007;BGEAED_01073;BHJHEC_03981;BKLOHC_01956;BPLIPK_03787;CBPCJH_00767;CKHCDK_03907;DBCCLE_04046;DPLIOB_03468;EEGMED_03864;EEMIBL_02760;FDDMPP_04033;FGOACM_03626;FLEJOH_00579;FNLDAG_03546;FOMADB_03904;GAGFCG_01314;GKEIOM_01270;GKLDEJ_03609;HBIPEG_00830;HEJICF_03823;HFAJAL_00243;HFPBEP_03208;HIHJDO_02729;HLEDKO_03904 | CRISPR-associated endoribonuclease Cas2 | |||
| 22 | group_1420 | gene_presence_absence | PPE53 | group_1420 | Rv3159c | none confidence | PPE53 | PPE family protein PPE53 | Rv3159c | PPE53 | PPE family protein PPE53 | none | 50.27 | 19.16 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=50.27; coverage=19.16 | 49 | 50 | 0.9800 | 13 | 50 | 0.2600 | cases (rpoB 763031 T C present) | 4.39 | 91.6667 | 16.1-522 | 16.0982 | 521.968 | 0.00137 | 12.3816 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(3527391..3529163) | matched_representative_sequence=group_1420 | AEMPHK_04108;AFNKCG_04190;ANMCAC_04061;APAKNA_03299;BHJHEC_02239;BKLOHC_02971;BPEJMN_03033;CIMEKD_04113;CKHCDK_01833;DJMHJN_00375;DNOEHN_02931;DPLIOB_00179;EBKMEK_02878;EEMIBL_00962;EOJHMN_04107;EPBFME_04097;FDDMPP_00689;FNACPH_04097;FNLDAG_04135;GNKHBM_03409;HEJICF_00856;HFPBEP_04071;HIHJDO_01098;HLIGOK_03233;HNJHNP_03351;ICLPCH_04120;IDADDB_01187;IEDNOI_02834;IJGDKF_03559;IJKJHL_02157 | PPE family protein PPE53 | ||
| 23 | group_2775 | gene_presence_absence | Rv3517 (group_2775) | group_2775 | Rv3517 | high confidence | group_2775 | hypothetical protein;DUF559 domain-containing protein | Rv3517 | hypothetical protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 41 | 50 | 0.8200 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -4.58 | 0.0432517 | 0.002444-0.7654 | 0.00244409 | 0.765401 | 7.39e-05 | 11.6625 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 3953431..3954270 | matched_representative_sequence=group_2775 | AEDLOG_01777;AEMPHK_02125;AFKOAF_01295;ANMCAC_01695;APAKNA_02845;BDILPO_02516;BDMCKA_02076;BGEAED_02063;BHJHEC_02004;BKLOHC_00818;BPEJMN_01902;BPLIPK_02356;CBPCJH_02365;CIMEKD_01985;DBCCLE_01783;DJMHJN_02721;DNOEHN_01515;DOFGLF_02498;DPLIOB_02072;EBKMEK_01275;EEGMED_00992;EEMIBL_02765;EOJHMN_01771;EPBFME_01227;FGOACM_01797;FLEJOH_01627;FNACPH_01434;FNLDAG_02689;FOMADB_03282;GAGFCG_02624 | hypothetical protein | |||
| 24 | group_1439 | gene_presence_absence | PPE15 | group_1439 | Rv1039c | none confidence | PPE15 | Sulfite oxidase-like oxidoreductase | Rv1039c | PPE15 | PPE family protein PPE15 | none | 35.79 | 1.45 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=35.79; coverage=1.45 | 6 | 50 | 0.1200 | 32 | 50 | 0.6400 | controls (rpoB 763031 T C absent) | -2.98 | 0.0831461 | 0.03054-0.2264 | 0.0305389 | 0.226376 | 1.25e-05 | 11.4913 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(1161297..1162472) | matched_representative_sequence=group_1439 | AEDLOG_04067;APAKNA_04002;BDMCKA_04010;BKLOHC_02716;BPLIPK_04023;CKHCDK_04015;DPLIOB_04003;EEGMED_03831;EEMIBL_04057;FGOACM_03981;FLEJOH_03959;FNLDAG_03780;GAGFCG_04059;GKEIOM_04023;HFPBEP_03199;HIHJDO_02936;ICLPCH_03556;IJGDKF_04004;ILFCIO_03927;IOJEPD_01115;IPDLAB_02369;JEBLOM_02250;JFHJPL_04050;JFNAAB_03925;KBDFIK_00696;LFDDMP_01570;LNDNPG_04016;MHDACH_03936;NEGAKJ_03902;NEKGNJ_04013 | PPE family protein PPE15 | ||
| 25 | group_747 | gene_presence_absence | group_747 | group_747 | Rv2618 | none confidence | group_747 | hypothetical protein;GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol dimannoside mannosyltransferase | Rv2618 | hypothetical protein | none | 29.50 | 1.31 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=29.50; coverage=1.31 | 6 | 50 | 0.1200 | 32 | 50 | 0.6400 | controls (rpoB 763031 T C absent) | -2.98 | 0.0831461 | 0.03054-0.2264 | 0.0305389 | 0.226376 | 1.25e-05 | 11.4913 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2946434..2947111 | matched_representative_sequence=group_747 | AEDLOG_04068;APAKNA_04001;BDMCKA_04011;BKLOHC_02715;BPLIPK_04024;CKHCDK_04016;DPLIOB_04004;EEGMED_03830;EEMIBL_04058;FGOACM_03980;FLEJOH_03958;FNLDAG_03781;GAGFCG_04058;GKEIOM_04022;HFPBEP_03200;HIHJDO_02937;ICLPCH_03557;IJGDKF_04003;ILFCIO_03928;IOJEPD_01114;IPDLAB_02370;JEBLOM_02249;JFHJPL_04051;JFNAAB_03926;KBDFIK_00697;LFDDMP_01569;LNDNPG_04017;MHDACH_03935;NEGAKJ_03903;NEKGNJ_04012 | hypothetical protein | |||
| 26 | group_81 | gene_presence_absence | Rv2633c (group_81) | group_81 | Rv2633c | high confidence | group_81 | Membrane transport protein MMPL domain-containing protein | Rv2633c | hypothetical protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 6 | 50 | 0.1200 | 32 | 50 | 0.6400 | controls (rpoB 763031 T C absent) | -2.98 | 0.0831461 | 0.03054-0.2264 | 0.0305389 | 0.226376 | 1.25e-05 | 11.4913 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(2959335..2959820) | matched_representative_sequence=group_810 | AEDLOG_04066;APAKNA_04003;BDMCKA_04009;BKLOHC_02717;BPLIPK_04022;CKHCDK_04014;DPLIOB_04002;EEGMED_03832;EEMIBL_04056;FGOACM_03982;FLEJOH_03960;FNLDAG_03779;GAGFCG_04060;GKEIOM_04024;HFPBEP_03198;HIHJDO_02935;ICLPCH_03555;IJGDKF_04005;ILFCIO_03926;IOJEPD_01116;IPDLAB_02368;JEBLOM_02251;JFHJPL_04049;JFNAAB_03924;KBDFIK_00695;LFDDMP_01571;LNDNPG_04015;MHDACH_03937;NEGAKJ_03901;NEKGNJ_04014 | hypothetical protein | |||
| 27 | group_3019 | gene_presence_absence | group_3019 | group_3019 | Rv2509 | none confidence | group_3019 | short-chain type dehydrogenase/reductase | Rv2509 | short-chain type dehydrogenase/reductase | none | 20.60 | 6.13 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=20.60; coverage=6.13 | 13 | 50 | 0.2600 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 4.23 | 36.36 | 2.094-631.2 | 2.09447 | 631.209 | 0.00145 | 11.0229 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2824678..2825484 | matched_representative_sequence=group_3019 | 17_refound_732_pseudo;AEMPHK_04000;AFNKCG_03638;BPEJMN_04014;CIMEKD_04007;EOJHMN_03922;IDADDB_03510;IMGGMF_03898;JIEBBG_03604;LABCDH_03982;LEFJPD_04030;MILAMD_04001;NKKFEE_03972 | short-chain type dehydrogenase/reductase | |||
| 28 | group_3083 | gene_presence_absence | cut1 | group_3083 | Rv1758 | none confidence | cut1 | cutinase | Rv1758 | cut1 | cutinase | none | 40.36 | 6.20 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=40.36; coverage=6.20 | 8 | 50 | 0.1600 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 4.47 | 20.2 | 1.133-360.3 | 1.1325 | 360.299 | 0.000213 | 11.0079 | Panaroo/Bakta+GenBank | nucleotide_similarity | 1989042..1989566 | matched_representative_sequence=group_3083 | AFNKCG_02635;CKHCDK_00761;FDDMPP_02601;HEJICF_00438;HLIGOK_03797;JGDOPI_00546;OLKJCH_00838;ONNOIP_00679 | cutinase | ||
| 29 | group_1870 | gene_presence_absence | group_1870 | group_1870 | Rv1887 | none confidence | group_1870 | hypothetical protein | Rv1887 | hypothetical protein | none | 31.35 | 4.34 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=31.35; coverage=4.34 | 0 | 50 | 0.0000 | 14 | 50 | 0.2800 | controls (rpoB 763031 T C absent) | -3.05 | 0.0249232 | 0.00144-0.4314 | 0.00143991 | 0.431393 | 0.00214 | 10.9960 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2136258..2137400 | matched_representative_sequence=98_refound_2443 | 98_refound_2443;BDILPO_03794;DOFGLF_03843;EEMIBL_03964;FNLDAG_03973;HBIPEG_03779;HLEDKO_03235;IJGDKF_04064;ILFCIO_02348;IPDLAB_03823;NEKGNJ_03124;NFBOIH_03182;NJPOJP_01084;NOBKKO_03865 | hypothetical protein | |||
| 30 | group_2853 | gene_presence_absence | cut1 | group_2853 | Rv1758 | none confidence | cut1 | cutinase | Rv1758 | cut1 | cutinase | none | 30.00 | 6.27 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=30.00; coverage=6.27 | 12 | 50 | 0.2400 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 4.23 | 32.7922 | 1.882-571.3 | 1.88232 | 571.28 | 0.00145 | 10.8739 | Panaroo/Bakta+GenBank | nucleotide_similarity | 1989042..1989566 | matched_representative_sequence=group_2853 | AEMPHK_04001;AFNKCG_03639;BPEJMN_04015;CIMEKD_04008;EOJHMN_03921;IDADDB_03509;IMGGMF_03899;JIEBBG_03605;LABCDH_03983;LEFJPD_04029;MILAMD_04002;NKKFEE_03971 | cutinase | ||
| 31 | group_3121 | gene_presence_absence | PE_PGRS46 | group_3121 | Rv2634c | high confidence | PE_PGRS46 | PE-PGRS family protein PE_PGRS46 | Rv2634c | PE_PGRS46 | PE-PGRS family protein PE_PGRS46 | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 41 | 50 | 0.8200 | 45 | 50 | 0.9000 | controls (rpoB 763031 T C absent) | -6.86 | 0.528051 | 0.1704-1.637 | 0.170356 | 1.6368 | 1.32e-07 | 10.8007 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(2960105..2962441) | matched_representative_sequence=3_refound_326 | 12_refound_514;22_refound_891;3_refound_326;44_refound_1470;80_refound_2031_pseudo;94_refound_2299_pseudo;95_refound_2415;AEDLOG_03226;AEDLOG_03227;AEMPHK_03523;AFKOAF_02598;ANMCAC_01892;APAKNA_01292;BDILPO_03745;BDMCKA_03635;BGEAED_03796;BHJHEC_03641;BPEJMN_01212;BPLIPK_03075;CBPCJH_03618;CIMEKD_03588;CKHCDK_03775;DBCCLE_03633;DJMHJN_01401;DNOEHN_03550;DOFGLF_03351;DPLIOB_01887;EBKMEK_03896;EEGMED_01325;EEMIBL_03901 | PE-PGRS family protein PE_PGRS46 | ||
| 32 | group_3313 | gene_presence_absence | Rv3113 (group_3313) | group_3313 | Rv3113 | high confidence | group_3313 | phosphatase | Rv3113 | phosphatase | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 0 | 50 | 0.0000 | 19 | 50 | 0.3800 | controls (rpoB 763031 T C absent) | -2.64 | 0.0159939 | 0.0009324-0.2744 | 0.00093238 | 0.274357 | 0.0188 | 10.6922 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 3480074..3480742 | matched_representative_sequence=group_3313 | AFKOAF_04135;BDILPO_04095;BDMCKA_04098;BHJHEC_04103;BKLOHC_04148;CBPCJH_04104;DOFGLF_04088;FOMADB_04093;HBIPEG_04109;HLEDKO_04097;ILFCIO_04154;JEBLOM_04058;KBDFIK_03598;LFDDMP_04005;NJPOJP_04096;NMJEMD_04114;ODHDPD_04117;OJHMIJ_04115;PMNAOE_04115 | phosphatase | |||
| 33 | group_3127 | gene_presence_absence | group_3127 | group_3127 | no_reference_locus | none confidence | group_3127 | hypothetical protein;PPE family domain-containing protein | none | No confident reference gene assignment; report the stable Panaroo cluster ID. | no sequence identity/coverage evidence available | 12 | 50 | 0.2400 | 37 | 50 | 0.7400 | controls (rpoB 763031 T C absent) | -2.75 | 0.116883 | 0.04794-0.2849 | 0.0479444 | 0.284948 | 3.26e-05 | 10.5836 | Panaroo/Bakta | none | No confident GenBank reference match found. The cluster may be accessory, divergent, absent from the reference, or not represented in Panaroo sequence outputs. | 11_refound_473_pseudo;14_refound_637_pseudo;20_refound_856_pseudo;28_refound_951_pseudo;36_refound_1060_pseudo;38_refound_1090_pseudo;42_refound_1368_pseudo;51_refound_1560_pseudo;70_refound_1889_pseudo;73_refound_1921_pseudo;8_refound_427_pseudo;98_refound_2452_pseudo;99_refound_2465_pseudo;9_refound_443_pseudo;AEDLOG_02950;AFKOAF_00688;BGEAED_04077;BKLOHC_03755;BKLOHC_03756;CBPCJH_03005;CKHCDK_03361;DOFGLF_03971;DPLIOB_03500;EEGMED_00456;FDDMPP_02446;FGOACM_02056;GKEIOM_01268;HBIPEG_04064;HFAJAL_03275;HFPBEP_00012 | hypothetical protein;PPE family domain-containing protein | ||||||||
| 34 | group_3140 | gene_presence_absence | PE_PGRS43-like | group_3140 | Rv2490c | medium confidence | PE_PGRS43 | hypothetical protein;PE family protein | Rv2490c | PE_PGRS43 | PE-PGRS family protein PE_PGRS43 | medium | 99.21 | 71.37 | Medium-confidence GenBank rescue; inspect manually before biological interpretation. | identity=99.21; coverage=71.37 | 47 | 50 | 0.9400 | 40 | 50 | 0.8000 | Check manually | -8.82 | 3.51852 | 0.978-12.66 | 0.977975 | 12.6588 | 3.07e-06 | 10.3278 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(2801254..2806236) | matched_representative_sequence=group_3140 | AEDLOG_01526;AEDLOG_03776;AEDLOG_03777;AEDLOG_03778;AEDLOG_03779;AEMPHK_01973;AFKOAF_03100;AFKOAF_03101;AFKOAF_03391;AFNKCG_03262;AFNKCG_03263;AFNKCG_03264;AFNKCG_04058;ANMCAC_01071;APAKNA_00521;BDILPO_00943;BDMCKA_03594;BDMCKA_03595;BDMCKA_04013;BDMCKA_04103;BGEAED_02661;BHJHEC_02213;BHJHEC_02214;BHJHEC_03535;BHJHEC_03536;BPEJMN_01744;BPLIPK_01827;BPLIPK_03788;BPLIPK_03789;BPLIPK_04117 | PE-PGRS family protein PE_PGRS43 | ||
| 35 | group_3101 | gene_presence_absence | PE_PGRS4 | group_3101 | Rv0279c | none confidence | PE_PGRS4 | PE-PGRS family protein PE_PGRS4 | Rv0279c | PE_PGRS4 | PE-PGRS family protein PE_PGRS4 | none | 86.75 | 35.59 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=86.75; coverage=35.59 | 8 | 50 | 0.1600 | 25 | 50 | 0.5000 | controls (rpoB 763031 T C absent) | -2.77 | 0.2 | 0.07982-0.5011 | 0.0798233 | 0.501107 | 1.71e-05 | 10.0889 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(336560..339073) | matched_representative_sequence=5_refound_372 | 5_refound_372;AEDLOG_04138;AFKOAF_03643;AFNKCG_03875;APAKNA_03324;BDILPO_00057;BDMCKA_04054;BGEAED_04103;CBPCJH_04089;CKHCDK_04177;DOFGLF_02700;DPLIOB_04133;EEGMED_03291;FDDMPP_00057;FGOACM_04108;HBIPEG_00436;HFAJAL_04078;HIHJDO_04163;ICLPCH_04099;IDADDB_01434;IJGDKF_04103;IPDLAB_04118;JFHJPL_04119;KOLHLA_04104;LNDNPG_00058;MLLPLE_04046;NEKGNJ_03310;NFBOIH_04119;NMJEMD_02408;NOBKKO_04100 | PE-PGRS family protein PE_PGRS4 | ||
| 36 | group_2997 | gene_presence_absence | PPE34 | group_2997 | Rv1917c | none confidence | PPE34 | hypothetical protein;PPE family protein | Rv1917c | PPE34 | PPE family protein PPE34 | none | 94.64 | 39.68 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=94.64; coverage=39.68 | 49 | 50 | 0.9800 | 32 | 50 | 0.6400 | cases (rpoB 763031 T C present) | 2.63 | 18.7846 | 3.358-105.1 | 3.3577 | 105.09 | 0.00218 | 9.8930 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(2162932..2167311) | matched_representative_sequence=group_2997 | AEDLOG_01782;AEDLOG_03752;AEMPHK_03652;AEMPHK_03653;AFKOAF_01213;AFNKCG_02248;AFNKCG_03014;ANMCAC_01407;BDILPO_01674;BDILPO_03793;BDMCKA_01710;BHJHEC_02941;BKLOHC_00410;BPEJMN_03739;CIMEKD_01066;CIMEKD_03641;CIMEKD_04109;CKHCDK_03141;CKHCDK_03546;DBCCLE_03310;DBCCLE_04000;DBCCLE_04001;DJMHJN_01368;DJMHJN_03831;DJMHJN_04078;DNOEHN_01729;DNOEHN_01730;DOFGLF_01473;DOFGLF_03844;DPLIOB_03246 | PPE family protein PPE34 | ||
| 37 | group_3070 | gene_presence_absence | ;tnp | group_3070 | Rv1313c | high confidence | ;tnp | hypothetical protein;Transposase IS204/IS1001/IS1096/IS1165 DDE domain-containing protein;ISL3 family transposase;ISL3 family IS1557 transposase | Rv1313c | insertion sequence element IS1557 transposase | high | 100.00 | 100.00 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=100.00; coverage=100.00 | 44 | 50 | 0.8800 | 20 | 50 | 0.4000 | cases (rpoB 763031 T C present) | 2.18 | 10.1857 | 3.765-27.56 | 3.76464 | 27.5589 | 0.000471 | 9.6755 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(1468171..1469505) | matched_representative_sequence=group_3070 | AEMPHK_01614;AEMPHK_04123;AFNKCG_01057;ANMCAC_02367;ANMCAC_04075;BDMCKA_04088;BGEAED_03953;BKLOHC_00749;BKLOHC_01080;BPEJMN_01245;BPEJMN_04103;CIMEKD_04117;DBCCLE_04089;DJMHJN_01877;DJMHJN_04094;DNOEHN_03637;DNOEHN_04116;EBKMEK_01773;EBKMEK_04128;EEGMED_04171;EOJHMN_03529;EOJHMN_04130;EPBFME_02093;EPBFME_04106;FDDMPP_01665;FDDMPP_02341;FNACPH_02295;FNACPH_04107;FOMADB_04085;GAGFCG_04117 | insertion sequence element IS1557 transposase | |||
| 38 | group_3428 | gene_presence_absence | sppA | group_3428 | Rv0724 | none confidence | sppA | protease IV SppA | Rv0724 | sppA | protease IV SppA | none | 33.57 | 1.39 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=33.57; coverage=1.39 | 6 | 50 | 0.1200 | 30 | 50 | 0.6000 | controls (rpoB 763031 T C absent) | -2.18 | 0.0981765 | 0.03629-0.2656 | 0.036286 | 0.265629 | 0.000471 | 9.6755 | Panaroo/Bakta+GenBank | nucleotide_similarity | 815663..817534 | matched_representative_sequence=group_3428 | AEDLOG_04121;AFKOAF_04118;APAKNA_04093;BDILPO_04081;BHJHEC_04086;BPLIPK_04110;CBPCJH_04092;CKHCDK_04191;DOFGLF_04075;DPLIOB_04145;EEMIBL_04116;FGOACM_04123;FLEJOH_04130;FNLDAG_04156;GKLDEJ_04104;HBIPEG_04099;HEJICF_04146;HFAJAL_04083;HFPBEP_04114;HLEDKO_04087;HLIGOK_04125;IJGDKF_04108;IJKJHL_04167;IPDLAB_04124;JFHJPL_04101;JFNAAB_04128;JGDOPI_04190;LNDNPG_04116;NFBOIH_04156;NJPOJP_04078 | protease IV SppA | ||
| 39 | group_600 | gene_presence_absence | folP2 | group_600 | Rv1207 | none confidence | folP2 | dihydropteroate synthase | Rv1207 | folP2 | dihydropteroate synthase | none | 19.35 | 33.70 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=19.35; coverage=33.70 | 26 | 50 | 0.5200 | 43 | 50 | 0.8600 | controls (rpoB 763031 T C absent) | -3.67 | 0.186488 | 0.07213-0.4822 | 0.0721306 | 0.482152 | 5.79e-05 | 9.6602 | Panaroo/Bakta+GenBank | nucleotide_similarity | 1351191..1352147 | matched_representative_sequence=group_600 | AEDLOG_03546;AEMPHK_01725;AFKOAF_00426;APAKNA_02036;BDMCKA_03159;BGEAED_01754;BHJHEC_03183;BKLOHC_03263;BPEJMN_01356;BPLIPK_03510;CBPCJH_01772;CIMEKD_01454;DBCCLE_03070;DJMHJN_01766;DNOEHN_03358;DOFGLF_01162;DPLIOB_01473;EBKMEK_01662;EEGMED_03802;EEMIBL_02868;EOJHMN_02919;EPBFME_02204;FDDMPP_01777;FGOACM_02846;FLEJOH_02864;FNACPH_02402;FNLDAG_03386;FOMADB_03703;GAGFCG_02317;GKEIOM_01661 | dihydropteroate synthase | ||
| 40 | group_2808 | gene_presence_absence | PE_PGRS45-like (group_2808) | group_2808 | Rv2615c | low confidence | PE_PGRS45 | PE-PGRS family protein PE_PGRS45 | Rv2615c | PE_PGRS45 | PE-PGRS family protein PE_PGRS45 | low | 92.66 | 43.35 | Low-confidence GenBank rescue; treat as tentative and keep the Panaroo cluster ID. | identity=92.66; coverage=43.35 | 47 | 50 | 0.9400 | 41 | 50 | 0.8200 | Check manually | -8.35 | 3.10671 | 0.8514-11.34 | 0.851448 | 11.3356 | 1.23e-05 | 9.5455 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(2943600..2944985) | matched_representative_sequence=group_2808 | 12_refound_505_pseudo;AEDLOG_03206;AEMPHK_01845;AFKOAF_01648;ANMCAC_01912;APAKNA_01272;BDILPO_02203;BDMCKA_03591;BGEAED_00635;BHJHEC_03539;BPEJMN_01192;BPLIPK_03095;CBPCJH_01764;CIMEKD_01807;CKHCDK_01801;DBCCLE_03632;DJMHJN_01421;DNOEHN_02314;DOFGLF_01154;DPLIOB_01867;EBKMEK_02857;EEGMED_01305;EEMIBL_02545;EOJHMN_00068;EPBFME_01812;FDDMPP_01433;FGOACM_01434;FLEJOH_03699;FNACPH_02001;FNLDAG_03769 | PE-PGRS family protein PE_PGRS45 | ||
| 41 | group_331 | gene_presence_absence | group_331 | group_331 | Rv2680 | none confidence | group_331 | hypothetical protein | Rv2680 | hypothetical protein | none | 23.67 | 42.16 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=23.67; coverage=42.16 | 49 | 50 | 0.9800 | 31 | 50 | 0.6200 | cases (rpoB 763031 T C present) | 1.99 | 20.4286 | 3.659-114.1 | 3.65888 | 114.059 | 0.0106 | 9.3272 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2996105..2996737 | matched_representative_sequence=22_refound_874 | 17_refound_683_pseudo;18_refound_767_pseudo;22_refound_874;23_refound_892_pseudo;33_refound_998;43_refound_1370_pseudo;46_refound_1483;47_refound_1503_pseudo;56_refound_1612_pseudo;58_refound_1645_pseudo;5_refound_354_pseudo;62_refound_1722_pseudo;63_refound_1733_pseudo;64_refound_1752_pseudo;67_refound_1809_pseudo;69_refound_1837_pseudo;71_refound_1890_pseudo;74_refound_1922;81_refound_2032;82_refound_2062_pseudo;85_refound_2120;87_refound_2142_pseudo;88_refound_2161;8_refound_410_pseudo;9_refound_428_pseudo;AEDLOG_02535;AFNKCG_02308;BHJHEC_00320;BPLIPK_00031;CKHCDK_03171 | hypothetical protein | |||
| 42 | group_3058 | gene_presence_absence | PE_PGRS57 | group_3058 | Rv3514 | none confidence | PE_PGRS57 | PE-PGRS family protein PE_PGRS57 | Rv3514 | PE_PGRS57 | PE-PGRS family protein PE_PGRS57 | none | 61.86 | 36.26 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=61.86; coverage=36.26 | 45 | 50 | 0.9000 | 35 | 50 | 0.7000 | Check manually | -5.18 | 3.61204 | 1.242-10.5 | 1.24241 | 10.5012 | 3.64e-05 | 9.2917 | Panaroo/Bakta+GenBank | nucleotide_similarity | 3945794..3950263 | matched_representative_sequence=group_3058 | AEDLOG_02224;AEDLOG_03443;AEMPHK_02560;AEMPHK_04119;AFKOAF_01912;AFKOAF_01913;AFKOAF_04116;AFNKCG_04221;ANMCAC_02837;ANMCAC_04068;APAKNA_02849;APAKNA_02973;APAKNA_02974;BDILPO_01470;BDILPO_04078;BGEAED_02067;BGEAED_02923;BPEJMN_02358;BPEJMN_04094;BPLIPK_02431;BPLIPK_02432;CBPCJH_02559;CBPCJH_02560;CIMEKD_02453;CIMEKD_04125;CKHCDK_01120;CKHCDK_01121;CKHCDK_04193;DJMHJN_02963;DJMHJN_04082 | PE-PGRS family protein PE_PGRS57 | ||
| 43 | cut1 | gene_presence_absence | cut1 | cut1 | Rv1758 | high confidence | ;cut1 | hypothetical protein;Cutinase cut1;cutinase Cut1 | Rv1758 | cut1 | cutinase | high | 100.0 | 100.0 | High-confidence GenBank-supported annotation. | identity=100.0; coverage=100.0 | 11 | 50 | 0.2200 | 36 | 50 | 0.7200 | controls (rpoB 763031 T C absent) | -2.09 | 0.115658 | 0.04725-0.2831 | 0.0472464 | 0.283128 | 0.000781 | 9.2194 | Panaroo/Bakta+GenBank | qualifier_exact | 1989042..1989566 | AEDLOG_04065;AFKOAF_04091;APAKNA_04004;BDILPO_04023;BDMCKA_04008;BDMCKA_04104;BKLOHC_02718;BKLOHC_04172;BPLIPK_04021;BPLIPK_04104;CBPCJH_04047;CKHCDK_04013;CKHCDK_04180;DOFGLF_04006;DPLIOB_04001;EEGMED_03833;EEMIBL_04055;FLEJOH_03961;FNLDAG_03778;FOMADB_04097;GAGFCG_04061;GKEIOM_04112;HEJICF_04149;HFPBEP_03197;HIHJDO_02934;HLEDKO_04118;HLIGOK_04028;ICLPCH_03554;IJGDKF_04006;ILFCIO_03925 | cutinase | |||
| 44 | group_1513 | gene_presence_absence | PE13 | group_1513 | Rv1195 | none confidence | PE13 | hypothetical protein;PE domain-containing protein | Rv1195 | PE13 | PE family protein PE13 | none | 50.24 | 5.11 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=50.24; coverage=5.11 | 48 | 50 | 0.9600 | 25 | 50 | 0.5000 | cases (rpoB 763031 T C present) | 1.88 | 19.4 | 4.858-77.47 | 4.85817 | 77.4696 | 0.0228 | 8.9200 | Panaroo/Bakta+GenBank | nucleotide_similarity | 1339003..1339302 | matched_representative_sequence=group_1513 | AEMPHK_03384;AFNKCG_01903;ANMCAC_04045;APAKNA_03568;BDILPO_03249;BGEAED_02727;BHJHEC_04012;BPEJMN_04055;CIMEKD_03439;CKHCDK_04038;DBCCLE_02876;DJMHJN_04057;DNOEHN_04079;EBKMEK_04093;EEGMED_03020;EOJHMN_04063;EPBFME_04077;FDDMPP_03058;FGOACM_02701;FNACPH_04069;GAGFCG_04068;GKEIOM_04069;GKLDEJ_01188;GNKHBM_04095;HEJICF_04022;HIHJDO_03543;HLIGOK_04114;HNJHNP_04085;ICLPCH_03098;IDADDB_03997 | PE family protein PE13 | ||
| 45 | group_2236 | gene_presence_absence | esxO | group_2236 | Rv2346c | none confidence | esxO | ESAT-6 like protein EsxO | Rv2346c | esxO | ESAT-6 like protein EsxO | none | 40.20 | 4.89 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=40.20; coverage=4.89 | 2 | 50 | 0.0400 | 10 | 50 | 0.2000 | Check manually | 5.84 | 0.198822 | 0.04706-0.84 | 0.0470579 | 0.840032 | 0.000454 | 8.6734 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(2625888..2626172) | matched_representative_sequence=group_2236 | 0_refound_51_pseudo;13_refound_551_pseudo;3_refound_242_pseudo;95_refound_2330_pseudo;FNLDAG_02893;FOMADB_02364;HFPBEP_02402;JIEBBG_03035;NGOKMK_02598;NJPOJP_02349;NNCHJK_02455;OJHMIJ_02527 | ESAT-6 like protein EsxO | ||
| 46 | group_3418 | gene_presence_absence | group_3418 | group_3418 | Rv3103c | none confidence | group_3418 | hypothetical protein | Rv3103c | hypothetical protein | none | 34.12 | 2.58 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=34.12; coverage=2.58 | 3 | 50 | 0.0600 | 7 | 50 | 0.1400 | Check manually | 8.47 | 0.427368 | 0.1126-1.622 | 0.112601 | 1.62204 | 3.94e-05 | 8.6310 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(3471413..3471850) | matched_representative_sequence=group_3418 | BKLOHC_04183;FOMADB_04105;HFPBEP_04158;JEBLOM_04132;JIEBBG_04138;LPCJNG_04174;NJPOJP_04113;NNCHJK_04166;OHPLLA_08119;OJHMIJ_04130 | hypothetical protein | |||
| 47 | group_2734 | gene_presence_absence | Rv1004c (group_2734) | group_2734 | Rv1004c | high confidence | group_2734 | membrane protein | Rv1004c | membrane protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 49 | 50 | 0.9800 | 40 | 50 | 0.8000 | Check manually | -6.83 | 8.55556 | 1.471-49.75 | 1.47119 | 49.754 | 0.00399 | 8.4959 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(1120889..1122148) | matched_representative_sequence=2_refound_189 | 20_refound_851;2_refound_189;59_refound_1682_pseudo;70_refound_1882;AEDLOG_02820;AEMPHK_02865;AFKOAF_02553;AFNKCG_01412;ANMCAC_03186;APAKNA_02875;BDILPO_03118;BDMCKA_02315;BGEAED_00609;BHJHEC_02307;BPEJMN_02458;BPLIPK_01984;CBPCJH_02394;CIMEKD_02756;CKHCDK_01718;DBCCLE_02053;DJMHJN_00590;DNOEHN_02340;DOFGLF_02672;DPLIOB_02162;EBKMEK_02948;EEGMED_01438;EEMIBL_03287;EOJHMN_00042;EPBFME_02800;FDDMPP_00774 | membrane protein | |||
| 48 | group_1373 | gene_presence_absence | PE_PGRS17 | group_1373 | Rv0978c | none confidence | PE_PGRS17 | PE-PGRS family protein PE_PGRS17 | Rv0978c | PE_PGRS17 | PE-PGRS family protein PE_PGRS17 | none | 21.42 | 3.78 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=21.42; coverage=3.78 | 1 | 50 | 0.0200 | 10 | 50 | 0.2000 | Check manually | 6.83 | 0.116883 | 0.0201-0.6797 | 0.0200989 | 0.679722 | 0.00399 | 8.4959 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(1093361..1094356) | matched_representative_sequence=group_1373 | BKLOHC_03847;FOMADB_00411;HFPBEP_00114;JEBLOM_00109;KBDFIK_03875;LFDDMP_04139;LPCJNG_00736;NJPOJP_03813;NNCHJK_01558;ODNJBD_00716;OJHMIJ_01400 | PE-PGRS family protein PE_PGRS17 | ||
| 49 | group_2207 | gene_presence_absence | aroF | group_2207 | Rv2540c | high confidence | aroF | Chorismate synthase | Rv2540c | aroF | chorismate synthase | high | 100.00 | 96.87 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=96.87 | 49 | 50 | 0.9800 | 41 | 50 | 0.8200 | Check manually | -7.29 | 7.55422 | 1.286-44.38 | 1.28574 | 44.3838 | 0.00278 | 8.4732 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(2863207..2864412) | matched_representative_sequence=group_2207 | AEDLOG_02121;AEMPHK_01921;AFKOAF_02053;AFNKCG_01708;ANMCAC_01988;APAKNA_01194;BDILPO_02280;BDMCKA_03442;BGEAED_00712;BHJHEC_01970;BPEJMN_01116;BPLIPK_02157;CBPCJH_01687;CIMEKD_01731;CKHCDK_02647;DBCCLE_01508;DJMHJN_01497;DNOEHN_02260;DOFGLF_01077;DPLIOB_02761;EBKMEK_03497;EEGMED_02441;EEMIBL_02622;EOJHMN_00145;EPBFME_01736;FDDMPP_01510;FGOACM_02361;FLEJOH_02984;FNACPH_01925;FNLDAG_03431 | chorismate synthase | ||
| 50 | group_1760 | gene_presence_absence | Rv2159c (group_1760) | group_1760 | Rv2159c | high confidence | group_1760 | Alkyl hydroperoxide reductase Rv2159c | Rv2159c | hypothetical protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 49 | 50 | 0.9800 | 41 | 50 | 0.8200 | Check manually | -7.29 | 7.55422 | 1.286-44.38 | 1.28574 | 44.3838 | 0.00278 | 8.4732 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(2420631..2421665) | matched_representative_sequence=group_1760 | AEDLOG_03816;AEMPHK_00197;AFKOAF_01905;AFNKCG_02015;ANMCAC_03145;APAKNA_01016;BDILPO_02835;BDMCKA_03403;BGEAED_01313;BHJHEC_03379;BPEJMN_03572;BPLIPK_03697;CBPCJH_01542;CIMEKD_00252;CKHCDK_02923;DBCCLE_04025;DJMHJN_02545;DNOEHN_03573;DOFGLF_02293;DPLIOB_03224;EBKMEK_02115;EEGMED_00812;EEMIBL_00178;EOJHMN_02165;EPBFME_00058;FDDMPP_02795;FGOACM_03072;FLEJOH_03788;FNACPH_03240;FNLDAG_02165 | hypothetical protein | |||
| 51 | menF | gene_presence_absence | Rv1005c (menF) | menF | Rv1005c | high confidence | menF | Isochorismate synthase MenF | Rv1005c | para-aminobenzoate synthase component I | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 49 | 50 | 0.9800 | 41 | 50 | 0.8200 | Check manually | -7.29 | 7.55422 | 1.286-44.38 | 1.28574 | 44.3838 | 0.00278 | 8.4732 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(1122222..1123598) | matched_representative_sequence=menF | AEDLOG_02819;AEMPHK_02866;AFKOAF_02552;AFNKCG_01411;ANMCAC_03187;APAKNA_02876;BDILPO_03117;BDMCKA_02316;BGEAED_00608;BHJHEC_02308;BPEJMN_02459;BPLIPK_01983;CBPCJH_02395;CIMEKD_02757;CKHCDK_01717;DBCCLE_02054;DJMHJN_00591;DNOEHN_02341;DOFGLF_02671;DPLIOB_02163;EBKMEK_02949;EEGMED_01437;EEMIBL_03288;EOJHMN_00041;EPBFME_02801;FDDMPP_00773;FGOACM_01971;FLEJOH_01957;FNACPH_02537;FNLDAG_04024 | para-aminobenzoate synthase component I | |||
| 52 | group_777 | gene_presence_absence | murG-like (group_777) | group_777 | Rv2153c | low confidence | murG | hypothetical protein;UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase | Rv2153c | murG | UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol-N-acetylglucosaminetransferase | low | 100.00 | 44.24 | Low-confidence GenBank rescue; treat as tentative and keep the Panaroo cluster ID. | identity=100.00; coverage=44.24 | 49 | 50 | 0.9800 | 41 | 50 | 0.8200 | Check manually | -7.29 | 7.55422 | 1.286-44.38 | 1.28574 | 44.3838 | 0.00278 | 8.4732 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(2412119..2413351) | matched_representative_sequence=group_777 | AEDLOG_03810;AEMPHK_00203;AFKOAF_01899;AFNKCG_02009;ANMCAC_03139;APAKNA_01022;BDILPO_02829;BDMCKA_03409;BGEAED_01307;BHJHEC_03373;BPEJMN_03566;BPLIPK_03703;CBPCJH_01548;CIMEKD_00246;CKHCDK_02917;DBCCLE_03389;DJMHJN_02551;DNOEHN_03579;DOFGLF_02299;DPLIOB_03218;EBKMEK_02109;EEGMED_00806;EEMIBL_00184;EOJHMN_02159;EPBFME_00052;FDDMPP_02801;FGOACM_03078;FLEJOH_03782;FNACPH_03234;FNLDAG_03110 | UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol-N-acetylglucosaminetransferase | ||
| 53 | group_504 | gene_presence_absence | PPE30 | group_504 | Rv1802 | high confidence | PPE30 | Uncharacterized PPE family protein PPE30 | Rv1802 | PPE30 | PPE family protein PPE30 | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 49 | 50 | 0.9800 | 41 | 50 | 0.8200 | Check manually | -7.29 | 7.55422 | 1.286-44.38 | 1.28574 | 44.3838 | 0.00278 | 8.4732 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 2043384..2044775 | matched_representative_sequence=group_504 | AEDLOG_03907;AEMPHK_01469;AFKOAF_01371;AFNKCG_03952;ANMCAC_01496;APAKNA_00974;BDILPO_01796;BDMCKA_02641;BGEAED_02403;BHJHEC_02897;BPEJMN_03724;BPLIPK_02947;CBPCJH_01400;CIMEKD_01186;CKHCDK_04079;DBCCLE_03580;DJMHJN_01248;DNOEHN_02645;DOFGLF_03491;DPLIOB_04096;EBKMEK_03841;EEGMED_03359;EEMIBL_02020;EOJHMN_03295;EPBFME_01267;FDDMPP_00960;FGOACM_03500;FLEJOH_04033;FNACPH_01559;FNLDAG_04056 | PPE family protein PPE30 | ||
| 54 | group_563 | gene_presence_absence | group_563 | group_563 | Rv0025 | none confidence | group_563 | hypothetical protein | Rv0025 | hypothetical protein | none | 35.03 | 1.53 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=35.03; coverage=1.53 | 1 | 50 | 0.0200 | 9 | 50 | 0.1800 | Check manually | 7.29 | 0.132376 | 0.02253-0.7778 | 0.0225307 | 0.77776 | 0.00278 | 8.4732 | Panaroo/Bakta+GenBank | nucleotide_similarity | 29245..29607 | matched_representative_sequence=12_refound_477 | 12_refound_477;41_refound_1318;BKLOHC_02581;JEBLOM_04174;KBDFIK_03935;LFDDMP_04168;LPCJNG_04203;NNCHJK_04079;ODNJBD_04195;OJHMIJ_04035 | hypothetical protein | |||
| 55 | group_3020 | gene_presence_absence | PE_PGRS29 | group_3020 | Rv1468c | high confidence | PE_PGRS29 | hypothetical protein;PE family protein | Rv1468c | PE_PGRS29 | PE-PGRS family protein PE_PGRS29 | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 48 | 50 | 0.9600 | 45 | 50 | 0.9000 | Check manually | -15.3 | 2.34505 | 0.4983-11.04 | 0.498336 | 11.0353 | 5.78e-05 | 8.4677 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(1655609..1656721) | matched_representative_sequence=2_refound_193 | 12_refound_511;2_refound_193;36_refound_1055_pseudo;37_refound_1067_pseudo;41_refound_1358;83_refound_2107_pseudo;94_refound_2294_pseudo;95_refound_2407;AEDLOG_01061;AEMPHK_03873;AFKOAF_00109;AFNKCG_01011;ANMCAC_03919;APAKNA_02694;BDILPO_01564;BDMCKA_03722;BGEAED_01372;BHJHEC_03721;BPEJMN_03931;BPLIPK_03882;CBPCJH_01430;CIMEKD_03884;CKHCDK_03599;DJMHJN_04003;DNOEHN_03810;DOFGLF_00822;DPLIOB_00745;EBKMEK_03803;EEGMED_00011;EEMIBL_03129 | PE-PGRS family protein PE_PGRS29 | ||
| 56 | group_3135 | gene_presence_absence | PE_PGRS22 | group_3135 | Rv1091 | none confidence | PE_PGRS22 | hypothetical protein;PE family protein | Rv1091 | PE_PGRS22 | PE-PGRS family protein PE_PGRS22 | none | 99.80 | 37.90 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=99.80; coverage=37.90 | 47 | 50 | 0.9400 | 36 | 50 | 0.7200 | Check manually | -4.67 | 5.39139 | 1.553-18.71 | 1.55325 | 18.7137 | 0.000999 | 8.4311 | Panaroo/Bakta+GenBank | nucleotide_similarity | 1216469..1219030 | matched_representative_sequence=group_3135 | AEDLOG_03118;AEDLOG_04088;AEMPHK_03306;AEMPHK_03742;AFKOAF_03638;AFNKCG_01483;ANMCAC_03551;ANMCAC_03839;APAKNA_03433;APAKNA_03870;BDILPO_02373;BDMCKA_02679;BGEAED_03198;BGEAED_04089;BHJHEC_02758;BPEJMN_02286;BPLIPK_03181;BPLIPK_04087;CBPCJH_03171;CBPCJH_04061;CIMEKD_03234;CIMEKD_03773;CIMEKD_03774;CKHCDK_00884;CKHCDK_04217;DBCCLE_02450;DJMHJN_02276;DNOEHN_03093;DNOEHN_04048;DOFGLF_01304 | PE-PGRS family protein PE_PGRS22 | ||
| 57 | group_2937 | gene_presence_absence | cobG-like (group_2937) | group_2937 | Rv2064 | low confidence | cobG | hypothetical protein;Precorrin-3B synthase | Rv2064 | cobG | precorrin-3B synthase | low | 99.91 | 51.92 | Low-confidence GenBank rescue; treat as tentative and keep the Panaroo cluster ID. | identity=99.91; coverage=51.92 | 49 | 50 | 0.9800 | 42 | 50 | 0.8400 | Check manually | -7.8 | 6.6 | 1.109-39.28 | 1.10908 | 39.2759 | 0.00212 | 8.3961 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2321451..2322542 | matched_representative_sequence=group_2937 | 82_refound_2095_pseudo;AEDLOG_03683;AEMPHK_03401;AFKOAF_02781;AFNKCG_01961;ANMCAC_03486;APAKNA_01112;BDILPO_03570;BDMCKA_02928;BGEAED_01216;BHJHEC_03428;BPEJMN_03223;BPLIPK_02448;CBPCJH_01641;CIMEKD_03420;CKHCDK_03068;DBCCLE_02737;DJMHJN_03872;DNOEHN_02778;DOFGLF_03119;DPLIOB_03335;EBKMEK_02017;EEGMED_02891;EEMIBL_00274;EOJHMN_02988;EPBFME_03291;FDDMPP_03806;FGOACM_02937;FLEJOH_03353;FNACPH_03499 | precorrin-3B synthase | ||
| 58 | group_3244 | gene_presence_absence | Rv1356c (group_3244) | group_3244 | Rv1356c | high confidence | group_3244 | Uncharacterized protein Rv1356c | Rv1356c | hypothetical protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(1524029..1524820) | matched_representative_sequence=group_3244 | AEDLOG_02264;AEMPHK_03221;AFKOAF_03591;AFNKCG_01532;ANMCAC_02979;BDILPO_01511;BDMCKA_02112;BGEAED_02802;BHJHEC_02108;BKLOHC_01438;BPEJMN_02618;BPLIPK_02391;CBPCJH_02134;CIMEKD_03100;CKHCDK_01161;DBCCLE_01818;DJMHJN_03150;DNOEHN_03070;DOFGLF_02957;DPLIOB_01608;EBKMEK_02656;EEGMED_01095;EOJHMN_02435;EPBFME_02858;FDDMPP_01283;FGOACM_02753;FLEJOH_01182;FNACPH_03043;FNLDAG_01624;FOMADB_02486 | hypothetical protein | |||
| 59 | group_2719 | gene_presence_absence | moeY | group_2719 | Rv1355c | high confidence | moeY | hypothetical protein;Rv1355c family protein;THIF-type NAD/FAD binding fold domain-containing protein | Rv1355c | moeY | molybdopterin biosynthesis protein MoeY | high | 99.95 | 92.74 | High-confidence GenBank-supported annotation. | identity=99.95; coverage=92.74 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(1521885..1524032) | matched_representative_sequence=group_2719 | AEDLOG_02265;AEMPHK_03220;AFKOAF_03590;AFNKCG_01533;ANMCAC_02978;BDILPO_01512;BDMCKA_02110;BDMCKA_02111;BGEAED_02801;BHJHEC_02107;BKLOHC_01437;BPEJMN_02617;BPLIPK_02390;CBPCJH_02135;CIMEKD_03101;CKHCDK_01162;DBCCLE_01817;DJMHJN_03151;DNOEHN_03069;DOFGLF_02958;DPLIOB_01607;EBKMEK_02657;EEGMED_01096;EOJHMN_02434;EPBFME_02859;FDDMPP_01282;FGOACM_02752;FGOACM_03110;FLEJOH_01183;FNACPH_03044 | molybdopterin biosynthesis protein MoeY | ||
| 60 | group_2341 | gene_presence_absence | lprP | group_2341 | Rv0962c | none confidence | lprP | Uncharacterized protein Rv2277c | Rv0962c | lprP | lipoprotein LprP | none | 40.25 | 1.75 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=40.25; coverage=1.75 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(1074440..1075114) | matched_representative_sequence=group_2341 | AEDLOG_02584;AEMPHK_00077;AFKOAF_03272;AFNKCG_00619;ANMCAC_00965;BDILPO_00550;BDMCKA_01523;BGEAED_01890;BHJHEC_00917;BKLOHC_00999;BPEJMN_00539;BPLIPK_01467;CBPCJH_03700;CIMEKD_00372;CKHCDK_01019;DBCCLE_00440;DJMHJN_02127;DNOEHN_00117;DOFGLF_03743;DPLIOB_01717;EBKMEK_00518;EEGMED_00370;EOJHMN_00937;EPBFME_00178;FDDMPP_02617;FGOACM_02578;FLEJOH_01416;FNACPH_00851;FNLDAG_00252;FOMADB_01054 | lipoprotein LprP | ||
| 61 | cyp121 | gene_presence_absence | cyp121 | cyp121 | Rv2276 | high confidence | ;cyp121 | hypothetical protein;Mycocyclosin synthase;mycocyclosin synthase Cyp121 | Rv2276 | cyp121 | cytochrome P450 Cyp121 | high | 100.0 | 100.0 | High-confidence GenBank-supported annotation. | identity=100.0; coverage=100.0 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | qualifier_exact | 2547749..2548939 | AEDLOG_02583;AEMPHK_00078;AFKOAF_03271;AFNKCG_00618;ANMCAC_00964;BDILPO_00549;BDMCKA_01524;BGEAED_01889;BHJHEC_00918;BKLOHC_01000;BPEJMN_00540;BPLIPK_01466;CBPCJH_03701;CIMEKD_00371;CKHCDK_01020;DBCCLE_00439;DJMHJN_02128;DNOEHN_00116;DOFGLF_03744;DPLIOB_01718;EBKMEK_00517;EEGMED_00369;EOJHMN_00938;EPBFME_00177;FDDMPP_02616;FGOACM_02579;FLEJOH_01417;FNACPH_00850;FNLDAG_00253;FOMADB_01053 | cytochrome P450 Cyp121 | |||
| 62 | group_2198 | gene_presence_absence | Rv2273-like (group_2198) | group_2198 | Rv2273 | medium confidence | group_2198 | Uncharacterized protein Rv2273 | Rv2273 | transmembrane protein | medium | 99.70 | 77.88 | Medium-confidence locus-level GenBank rescue. | identity=99.70; coverage=77.88 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2546102..2546431 | matched_representative_sequence=group_2198 | AEDLOG_02581;AEMPHK_00080;AFKOAF_03269;AFNKCG_00616;ANMCAC_00962;BDILPO_00547;BDMCKA_01526;BGEAED_01887;BHJHEC_00920;BKLOHC_01002;BPEJMN_00542;BPLIPK_01464;CBPCJH_03703;CIMEKD_00369;CKHCDK_01022;DBCCLE_00437;DJMHJN_02130;DNOEHN_00114;DOFGLF_03746;DPLIOB_01720;EBKMEK_00515;EEGMED_00367;EOJHMN_00940;EPBFME_00175;FDDMPP_02614;FGOACM_02581;FLEJOH_01419;FNACPH_00848;FNLDAG_00255;FOMADB_01051 | transmembrane protein | |||
| 63 | group_1858 | gene_presence_absence | Rv2272 (group_1858) | group_1858 | Rv2272 | high confidence | group_1858 | DUF202 domain-containing protein | Rv2272 | transmembrane protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 2545737..2546105 | matched_representative_sequence=group_1858 | AEDLOG_02580;AEMPHK_00081;AFKOAF_03268;AFNKCG_00615;ANMCAC_00961;BDILPO_00546;BDMCKA_01527;BGEAED_01886;BHJHEC_00921;BKLOHC_01003;BPEJMN_00543;BPLIPK_01463;CBPCJH_03704;CIMEKD_00368;CKHCDK_01023;DBCCLE_00436;DJMHJN_02131;DNOEHN_00113;DOFGLF_03747;DPLIOB_01721;EBKMEK_00514;EEGMED_00366;EOJHMN_00941;EPBFME_00174;FDDMPP_02613;FGOACM_02582;FLEJOH_01420;FNACPH_00847;FNLDAG_00256;FOMADB_01050 | transmembrane protein | |||
| 64 | group_1609 | gene_presence_absence | Rv2102 (group_1609) | group_1609 | Rv2102 | high confidence | group_1609 | hypothetical protein;Uncharacterized protein Rv2102 | Rv2102 | hypothetical protein | high | 100.00 | 85.97 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=85.97 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 2363391..2364107 | matched_representative_sequence=group_1609 | 95_refound_2370_pseudo;AEDLOG_03420;AEMPHK_03920;AFKOAF_03203;AFNKCG_03053;ANMCAC_03449;BDILPO_02775;BDMCKA_03932;BGEAED_01253;BHJHEC_03904;BKLOHC_00248;BPEJMN_03950;BPLIPK_02486;CBPCJH_01603;CIMEKD_03903;CKHCDK_03959;DBCCLE_03990;DJMHJN_02606;DNOEHN_02741;DOFGLF_02354;DPLIOB_04054;EBKMEK_02054;EEGMED_00751;EOJHMN_03798;EPBFME_03328;FDDMPP_02856;FGOACM_03282;FLEJOH_03504;FNACPH_03532;FNLDAG_03926 | hypothetical protein | |||
| 65 | group_1521 | gene_presence_absence | Rv2271 (group_1521) | group_1521 | Rv2271 | high confidence | group_1521 | hypothetical protein | Rv2271 | hypothetical protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 2545332..2545631 | matched_representative_sequence=group_1521 | AEDLOG_02579;AEMPHK_00082;AFKOAF_03267;AFNKCG_00614;ANMCAC_00960;BDILPO_00545;BDMCKA_01528;BGEAED_01885;BHJHEC_00922;BKLOHC_01004;BPEJMN_00544;BPLIPK_01462;CBPCJH_03705;CIMEKD_00367;CKHCDK_01024;DBCCLE_00435;DJMHJN_02132;DNOEHN_00112;DOFGLF_03748;DPLIOB_01722;EBKMEK_00513;EEGMED_00365;EOJHMN_00942;EPBFME_00173;FDDMPP_02612;FGOACM_02583;FLEJOH_01421;FNACPH_00846;FNLDAG_00257;FOMADB_01049 | hypothetical protein | |||
| 66 | group_962 | gene_presence_absence | Rv2275 (group_962) | group_962 | Rv2275 | high confidence | group_962 | hypothetical protein;Cyclo(L-tyrosyl-L-tyrosyl) synthase | Rv2275 | cyclo(L-tyrosyl-L-tyrosyl) synthase | high | 99.89 | 89.77 | High-confidence locus-level GenBank rescue. | identity=99.89; coverage=89.77 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2546883..2547752 | matched_representative_sequence=group_962 | AEDLOG_02582;AEMPHK_00079;AFKOAF_03270;AFNKCG_00617;ANMCAC_00963;BDILPO_00548;BDMCKA_01525;BGEAED_01888;BHJHEC_00919;BKLOHC_01001;BPEJMN_00541;BPLIPK_01465;CBPCJH_03702;CIMEKD_00370;CKHCDK_01021;DBCCLE_00438;DJMHJN_02129;DNOEHN_00115;DOFGLF_03745;DPLIOB_01719;EBKMEK_00516;EEGMED_00368;EOJHMN_00939;EPBFME_00176;FDDMPP_02615;FGOACM_02580;FLEJOH_01418;FNACPH_00849;FNLDAG_00254;FOMADB_01052 | cyclo(L-tyrosyl-L-tyrosyl) synthase | |||
| 67 | group_252 | gene_presence_absence | Rv0106 (group_252) | group_252 | Rv0106 | high confidence | group_252 | Diguanylate phosphodiesterase | Rv0106 | hypothetical protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 124374..125570 | matched_representative_sequence=group_2526 | AEDLOG_02266;AEMPHK_03219;AFKOAF_03589;AFNKCG_01534;ANMCAC_02977;BDILPO_01513;BDMCKA_02109;BGEAED_02800;BHJHEC_02106;BKLOHC_01436;BPEJMN_02616;BPLIPK_02389;CBPCJH_02136;CIMEKD_03102;CKHCDK_01163;DBCCLE_01816;DJMHJN_03152;DNOEHN_03068;DOFGLF_02959;DPLIOB_01606;EBKMEK_02658;EEGMED_01097;EOJHMN_02433;EPBFME_02860;FDDMPP_01281;FGOACM_03111;FLEJOH_01184;FNACPH_03045;FNLDAG_01622;FOMADB_02483 | hypothetical protein | |||
| 68 | group_324 | gene_presence_absence | Rv1356c (group_324) | group_324 | Rv1356c | high confidence | group_324 | hypothetical protein | Rv1356c | hypothetical protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 0 | 50 | 0.0000 | 6 | 50 | 0.1200 | controls (rpoB 763031 T C absent) | -2.49 | 0.0677837 | 0.003713-1.238 | 0.00371262 | 1.23757 | 0.0317 | 8.3819 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(1524029..1524820) | matched_representative_sequence=group_3244 | BGEAED_03305;BPLIPK_03331;FLEJOH_04157;GKEIOM_02891;IPDLAB_03394;NOBKKO_03681 | hypothetical protein | |||
| 69 | group_3081 | gene_presence_absence | PE_PGRS26 | group_3081 | Rv1441c | none confidence | PE_PGRS26 | hypothetical protein;PE family protein | Rv1441c | PE_PGRS26 | PE-PGRS family protein PE_PGRS26 | none | 51.13 | 28.05 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=51.13; coverage=28.05 | 43 | 50 | 0.8600 | 36 | 50 | 0.7200 | Check manually | -4.32 | 2.30411 | 0.8602-6.172 | 0.860232 | 6.1715 | 7.24e-05 | 8.3445 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(1618209..1619684) | matched_representative_sequence=group_3081 | AEDLOG_03489;AEDLOG_04050;AEMPHK_02514;AFKOAF_01959;AFKOAF_03763;AFNKCG_01177;ANMCAC_02791;APAKNA_02927;BDILPO_01424;BGEAED_02969;BGEAED_02970;BPEJMN_02404;BPLIPK_03456;BPLIPK_03996;CBPCJH_02512;CBPCJH_02513;CIMEKD_02499;CKHCDK_02021;DJMHJN_02917;DNOEHN_03244;DOFGLF_01485;DPLIOB_02523;EBKMEK_02569;EBKMEK_04019;EEGMED_02319;EEMIBL_02190;EEMIBL_02191;EOJHMN_02805;EPBFME_02685;FDDMPP_01369 | PE-PGRS family protein PE_PGRS26 | ||
| 70 | group_2884 | gene_presence_absence | Rv1066-like (group_2884) | group_2884 | Rv1066 | medium confidence | group_2884 | Rhodanese domain-containing protein;hypothetical protein | Rv1066 | hypothetical protein | medium | 91.43 | 82.43 | Medium-confidence locus-level GenBank rescue. | identity=91.43; coverage=82.43 | 49 | 50 | 0.9800 | 42 | 50 | 0.8400 | Check manually | -7.44 | 6.6 | 1.109-39.28 | 1.10908 | 39.2759 | 0.00255 | 8.3159 | Panaroo/Bakta+GenBank | nucleotide_similarity | 1187998..1188393 | matched_representative_sequence=group_2884 | AEDLOG_03931;AEMPHK_03851;AFKOAF_03441;AFNKCG_02881;ANMCAC_03941;APAKNA_03948;BDILPO_02400;BDMCKA_03744;BGEAED_03954;BHJHEC_03739;BPEJMN_02312;BPLIPK_03904;CBPCJH_03933;CIMEKD_03882;CKHCDK_03464;DBCCLE_03758;DJMHJN_02249;DNOEHN_03832;DOFGLF_01277;DPLIOB_03623;EBKMEK_03897;EEGMED_03416;EEMIBL_03994;EOJHMN_03773;EPBFME_03963;FDDMPP_02070;FGOACM_03592;FLEJOH_03394;FNACPH_03604;FNLDAG_03022 | hypothetical protein | |||
| 71 | group_2414 | gene_presence_absence | Rv0613c (group_2414) | group_2414 | Rv0613c | high confidence | group_2414 | hypothetical protein;Zinc-binding protein | Rv0613c | hypothetical protein | high | 99.96 | 84.93 | High-confidence locus-level GenBank rescue. | identity=99.96; coverage=84.93 | 49 | 50 | 0.9800 | 42 | 50 | 0.8400 | Check manually | -7.44 | 6.6 | 1.109-39.28 | 1.10908 | 39.2759 | 0.00255 | 8.3159 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(706948..709515) | matched_representative_sequence=group_2414 | 94_refound_2284_pseudo;AEDLOG_00612;AEMPHK_00292;AFKOAF_02664;AFNKCG_02540;ANMCAC_00194;APAKNA_03696;BDILPO_01951;BDMCKA_00652;BGEAED_01493;BHJHEC_01321;BPEJMN_00348;BPLIPK_00893;CBPCJH_01225;CIMEKD_01339;CKHCDK_00134;DBCCLE_01987;DJMHJN_00765;DNOEHN_00870;DOFGLF_00292;DPLIOB_02809;EBKMEK_00968;EEGMED_02084;EEMIBL_00395;EOJHMN_02093;EPBFME_00595;FDDMPP_00359;FGOACM_00393;FLEJOH_02628;FNACPH_00356 | hypothetical protein | |||
| 72 | group_3388 | gene_presence_absence | tatD | group_3388 | Rv1008 | none confidence | tatD | deoxyribonuclease TatD | Rv1008 | tatD | deoxyribonuclease TatD | none | 33.13 | 7.25 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=33.13; coverage=7.25 | 1 | 50 | 0.0200 | 8 | 50 | 0.1600 | Check manually | 7.29 | 0.151515 | 0.02546-0.9017 | 0.0254609 | 0.90165 | 0.00278 | 8.2784 | Panaroo/Bakta+GenBank | nucleotide_similarity | 1127089..1127883 | matched_representative_sequence=group_3388 | BKLOHC_04150;HFPBEP_04000;JEBLOM_04070;LFDDMP_04024;LPCJNG_04080;NJPOJP_03916;NNCHJK_03702;ODNJBD_04116;OJHMIJ_03954 | deoxyribonuclease TatD | ||
| 73 | group_3383 | gene_presence_absence | group_3383 | group_3383 | Rv1638A | none confidence | group_3383 | hypothetical protein | Rv1638A | hypothetical protein | none | 28.19 | 3.55 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=28.19; coverage=3.55 | 1 | 50 | 0.0200 | 8 | 50 | 0.1600 | Check manually | 7.29 | 0.151515 | 0.02546-0.9017 | 0.0254609 | 0.90165 | 0.00279 | 8.2769 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(1846716..1846973) | matched_representative_sequence=80_refound_1995 | 80_refound_1995;HFPBEP_04047;JEBLOM_03807;KBDFIK_03521;LFDDMP_03914;LPCJNG_03852;NJPOJP_04018;ODNJBD_04033;OJHMIJ_04030 | hypothetical protein | |||
| 74 | group_2903 | gene_presence_absence | PE_PGRS34 | group_2903 | Rv1840c | high confidence | PE_PGRS34 | hypothetical protein;PE family protein;Uncharacterized PE-PGRS family protein PE_PGRS34 | Rv1840c | PE_PGRS34 | PE-PGRS family protein PE_PGRS34 | high | 99.90 | 82.66 | High-confidence GenBank-supported annotation. | identity=99.90; coverage=82.66 | 48 | 50 | 0.9600 | 40 | 50 | 0.8000 | Check manually | -5.77 | 5.02963 | 1.19-21.25 | 1.19043 | 21.2504 | 0.00119 | 8.2549 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(2087971..2089518) | matched_representative_sequence=group_2903 | 82_refound_2094_pseudo;AEDLOG_01865;AEMPHK_01432;AFKOAF_01408;ANMCAC_01460;APAKNA_00938;BDILPO_01759;BDMCKA_03523;BGEAED_02366;BHJHEC_03493;BPEJMN_01699;BPLIPK_01592;CBPCJH_01363;CIMEKD_01149;CKHCDK_00387;DBCCLE_03449;DJMHJN_01285;DNOEHN_01813;DOFGLF_01389;DPLIOB_00283;EBKMEK_02202;EEGMED_02721;EEMIBL_01984;EOJHMN_01073;EPBFME_01304;FDDMPP_00997;FGOACM_01391;FLEJOH_01559;FNACPH_01522;FOMADB_03124 | PE-PGRS family protein PE_PGRS34 | ||
| 75 | group_2987 | gene_presence_absence | Rv2652c (group_2987) | group_2987 | Rv2652c | high confidence | group_2987 | hypothetical protein;phage terminase small subunit P27 family | Rv2652c | prophage protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 44 | 50 | 0.8800 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -4.23 | 0.0677837 | 0.003713-1.238 | 0.00371262 | 1.23757 | 0.0433 | 8.2464 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(2975928..2976554) | matched_representative_sequence=group_2987 | AEDLOG_03247;AEMPHK_03543;AFKOAF_02618;AFNKCG_03089;ANMCAC_01872;APAKNA_01312;BDILPO_03725;BDMCKA_03656;BGEAED_03816;BHJHEC_03620;BKLOHC_03953;BPEJMN_01232;BPLIPK_03055;CBPCJH_03598;CIMEKD_03568;CKHCDK_03586;DBCCLE_03654;DJMHJN_01381;DNOEHN_03530;DOFGLF_03371;DPLIOB_03677;EBKMEK_03863;EEGMED_03375;EEMIBL_03921;EOJHMN_03171;EPBFME_01847;FDDMPP_01393;FGOACM_03546;FLEJOH_03657;FNACPH_02041 | prophage protein | |||
| 76 | group_360 | gene_presence_absence | Rv2651c (group_360) | group_360 | Rv2651c | high confidence | group_360 | PhiRv2 prophage protease;Prohead serine protease domain-containing protein | Rv2651c | prophage protease | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 44 | 50 | 0.8800 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -4.23 | 0.0677837 | 0.003713-1.238 | 0.00371262 | 1.23757 | 0.0433 | 8.2464 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(2975242..2975775) | matched_representative_sequence=group_360 | AEDLOG_03246;AEMPHK_03542;AFKOAF_02617;AFNKCG_03090;ANMCAC_01873;APAKNA_01311;BDILPO_03726;BDMCKA_03655;BGEAED_03815;BHJHEC_03621;BKLOHC_03952;BPEJMN_01231;BPLIPK_03056;CBPCJH_03599;CIMEKD_03569;CKHCDK_03585;DBCCLE_03653;DJMHJN_01382;DNOEHN_03531;DOFGLF_03370;DPLIOB_03678;EBKMEK_03862;EEGMED_03376;EEMIBL_03920;EOJHMN_03172;EPBFME_01846;FDDMPP_01394;FGOACM_03547;FLEJOH_03658;FNACPH_02040 | prophage protease | |||
| 77 | group_3208 | gene_presence_absence | group_3208 | group_3208 | Rv0008c | none confidence | group_3208 | cell wall synthesis protein CwsA | Rv0008c | cell wall synthesis protein CwsA | none | 42.28 | 5.65 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=42.28; coverage=5.65 | 1 | 50 | 0.0200 | 7 | 50 | 0.1400 | Check manually | 8.18 | 0.175758 | 0.02906-1.063 | 0.029059 | 1.06304 | 0.00187 | 8.2365 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(11874..12311) | matched_representative_sequence=40_refound_1157 | 40_refound_1157;BKLOHC_03499;JEBLOM_03201;LFDDMP_02846;LPCJNG_03244;NJPOJP_03848;NNCHJK_03926;ODNJBD_03303 | cell wall synthesis protein CwsA | |||
| 78 | group_1834 | gene_presence_absence | PE18 | group_1834 | Rv1788 | none confidence | PE18 | PE family protein PE18 | Rv1788 | PE18 | PE family protein PE18 | none | 21.10 | 4.24 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=21.10; coverage=4.24 | 1 | 50 | 0.0200 | 7 | 50 | 0.1400 | Check manually | 8.18 | 0.175758 | 0.02906-1.063 | 0.029059 | 1.06304 | 0.00187 | 8.2365 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2026477..2026776 | matched_representative_sequence=group_1834 | BKLOHC_03500;JEBLOM_03202;KBDFIK_03991;LFDDMP_02845;LPCJNG_03245;NJPOJP_03849;NNCHJK_03925;ODNJBD_03302 | PE family protein PE18 | ||
| 79 | group_1734 | gene_presence_absence | group_1734 | group_1734 | Rv0108c | none confidence | group_1734 | Transposase IS701-like DDE domain-containing protein | Rv0108c | hypothetical protein | none | 46.71 | 6.49 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=46.71; coverage=6.49 | 11 | 50 | 0.2200 | 3 | 50 | 0.0600 | cases (rpoB 763031 T C present) | 3.11 | 3.95118 | 1.111-14.05 | 1.11098 | 14.0523 | 0.000606 | 8.1998 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(130895..131104) | matched_representative_sequence=group_1734 | AFNKCG_01943;CKHCDK_04194;FDDMPP_03822;HEJICF_02889;IJKJHL_03163;JGDOPI_02947;KBDFIK_02198;MHDACH_04162;MLLPLE_04088;NBJBMA_04125;NMJEMD_04096;OJOIGL_04141;OLKJCH_02957;ONNOIP_03965 | hypothetical protein | |||
| 80 | group_3375 | gene_presence_absence | group_3375 | group_3375 | Rv3069 | none confidence | group_3375 | fluoride ion transporter CrcB | Rv3069 | fluoride ion transporter CrcB | none | 39.15 | 4.90 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=39.15; coverage=4.90 | 1 | 50 | 0.0200 | 7 | 50 | 0.1400 | Check manually | 7.8 | 0.175758 | 0.02906-1.063 | 0.029059 | 1.06304 | 0.00212 | 8.1820 | Panaroo/Bakta+GenBank | nucleotide_similarity | 3433692..3434090 | matched_representative_sequence=group_3375 | JEBLOM_04030;KBDFIK_03577;LFDDMP_03834;LPCJNG_03999;NJPOJP_04039;NNCHJK_04095;ODNJBD_03975;OJHMIJ_04058 | fluoride ion transporter CrcB | |||
| 81 | group_1581 | gene_presence_absence | group_1581 | group_1581 | Rv0025 | none confidence | group_1581 | hypothetical protein | Rv0025 | hypothetical protein | none | 32.96 | 2.31 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=32.96; coverage=2.31 | 1 | 50 | 0.0200 | 7 | 50 | 0.1400 | Check manually | 7.36 | 0.175758 | 0.02906-1.063 | 0.029059 | 1.06304 | 0.00269 | 8.0786 | Panaroo/Bakta+GenBank | nucleotide_similarity | 29245..29607 | matched_representative_sequence=group_1581 | BKLOHC_03595;HFPBEP_03929;JEBLOM_03250;LFDDMP_03019;LPCJNG_03351;NNCHJK_03972;ODNJBD_03369;OJHMIJ_03903 | hypothetical protein | |||
| 82 | group_1005 | gene_presence_absence | bcpB | group_1005 | Rv1608c | none confidence | bcpB | peroxiredoxin | Rv1608c | bcpB | peroxiredoxin | none | 31.59 | 1.86 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=31.59; coverage=1.86 | 1 | 50 | 0.0200 | 7 | 50 | 0.1400 | Check manually | 7.36 | 0.175758 | 0.02906-1.063 | 0.029059 | 1.06304 | 0.00269 | 8.0786 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(1807298..1807762) | matched_representative_sequence=group_1005 | 13_refound_571_pseudo;3_refound_259_pseudo;95_refound_2355_pseudo;BKLOHC_03856;HFPBEP_02913;LFDDMP_03601;NNCHJK_02980;OJHMIJ_02933 | peroxiredoxin | ||
| 83 | group_335 | gene_presence_absence | Rv3054c (group_335) | group_335 | Rv3054c | high confidence | group_335 | hypothetical protein | Rv3054c | hypothetical protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 1 | 50 | 0.0200 | 7 | 50 | 0.1400 | Check manually | 7.36 | 0.175758 | 0.02906-1.063 | 0.029059 | 1.06304 | 0.00269 | 8.0786 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(3415435..3415989) | matched_representative_sequence=group_3358 | BKLOHC_02860;HFPBEP_03965;JEBLOM_03441;LFDDMP_04197;LPCJNG_03538;NNCHJK_03916;ODNJBD_03549;OJHMIJ_03868 | hypothetical protein | |||
| 84 | group_23 | gene_presence_absence | Rv3136A (group_23) | group_23 | Rv3136A | high confidence | group_23 | hypothetical protein | Rv3136A | hypothetical protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 1 | 50 | 0.0200 | 7 | 50 | 0.1400 | Check manually | 7.36 | 0.175758 | 0.02906-1.063 | 0.029059 | 1.06304 | 0.00269 | 8.0786 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(3502945..3503277) | matched_representative_sequence=group_2370 | BKLOHC_02861;HFPBEP_03966;JEBLOM_03440;LFDDMP_04196;LPCJNG_03539;NNCHJK_03917;ODNJBD_03548;OJHMIJ_03867 | hypothetical protein | |||
| 85 | group_2760 | gene_presence_absence | PE_PGRS28 | group_2760 | Rv1452c | none confidence | PE_PGRS28 | hypothetical protein;PE domain-containing protein | Rv1452c | PE_PGRS28 | PE-PGRS family protein PE_PGRS28 | none | 91.64 | 27.73 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=91.64; coverage=27.73 | 46 | 50 | 0.9200 | 41 | 50 | 0.8200 | Check manually | -6.93 | 2.36546 | 0.7145-7.832 | 0.714472 | 7.83153 | 0.000146 | 8.0778 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(1636004..1638229) | matched_representative_sequence=group_2760 | AEDLOG_01045;AEMPHK_04100;AEMPHK_04101;AFKOAF_00125;AFNKCG_01027;ANMCAC_04051;APAKNA_04080;BDILPO_04073;BDMCKA_04072;BDMCKA_04073;BGEAED_01356;BHJHEC_04077;BHJHEC_04078;BPEJMN_04080;BPLIPK_04097;BPLIPK_04098;CBPCJH_04081;CIMEKD_04093;CKHCDK_04155;CKHCDK_04156;DBCCLE_04114;DJMHJN_02904;DNOEHN_04086;DNOEHN_04087;DOFGLF_04059;DPLIOB_04131;DPLIOB_04132;EBKMEK_03787;EEGMED_04159;EEMIBL_04107 | PE-PGRS family protein PE_PGRS28 | ||
| 86 | recD | gene_presence_absence | recD | recD | Rv0629c | high confidence | recD | RecBCD enzyme subunit RecD | Rv0629c | recD | exonuclease V subunit alpha RecD | high | 100.0 | 100.0 | High-confidence GenBank-supported annotation. | identity=100.0; coverage=100.0 | 49 | 50 | 0.9800 | 43 | 50 | 0.8600 | Check manually | -7.29 | 5.68966 | 0.9407-34.41 | 0.940703 | 34.4128 | 0.00279 | 8.0627 | Panaroo/Bakta+GenBank | qualifier_exact | complement(720005..721732) | 0_refound_11_pseudo;13_refound_527_pseudo;AEDLOG_00628;AEMPHK_00308;AFKOAF_02648;AFNKCG_02524;ANMCAC_00178;APAKNA_03712;BDILPO_01967;BDMCKA_00636;BGEAED_01509;BHJHEC_01305;BPEJMN_00332;BPLIPK_00909;CBPCJH_01209;CIMEKD_01323;CKHCDK_00118;DBCCLE_01971;DJMHJN_00749;DNOEHN_00854;DOFGLF_00276;DPLIOB_02793;EBKMEK_00984;EEGMED_02100;EEMIBL_00411;EOJHMN_02109;EPBFME_00579;FDDMPP_00375;FGOACM_00409;FLEJOH_02644 | exonuclease V subunit alpha RecD | |||
| 87 | group_1321 | gene_presence_absence | group_1321 | group_1321 | Rv3430c | none confidence | group_1321 | transposase | Rv3430c | transposase | none | 35.48 | 3.03 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=35.48; coverage=3.03 | 1 | 50 | 0.0200 | 7 | 50 | 0.1400 | Check manually | 7.29 | 0.175758 | 0.02906-1.063 | 0.029059 | 1.06304 | 0.00279 | 8.0627 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(3847642..3848805) | matched_representative_sequence=group_1321 | HFPBEP_02139;JEBLOM_02640;KBDFIK_03131;LPCJNG_02849;NJPOJP_02045;NNCHJK_02284;ODNJBD_02831;OJHMIJ_02212 | transposase | |||
| 88 | group_2851 | gene_presence_absence | group_2851 | group_2851 | Rv0804 | none confidence | group_2851 | hypothetical protein | Rv0804 | hypothetical protein | none | 32.82 | 10.26 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=32.82; coverage=10.26 | 10 | 50 | 0.2000 | 36 | 50 | 0.7200 | controls (rpoB 763031 T C absent) | -1.48 | 0.102993 | 0.04139-0.2563 | 0.0413935 | 0.256264 | 0.0182 | 8.0193 | Panaroo/Bakta+GenBank | nucleotide_similarity | 898081..898710 | matched_representative_sequence=21_refound_872 | 21_refound_872;98_refound_2450;AEDLOG_04109;BDMCKA_04121;BGEAED_04131;BHJHEC_04122;BPLIPK_04145;CBPCJH_04121;CKHCDK_04176;DBCCLE_04116;DOFGLF_02699;DPLIOB_04172;EEGMED_04183;EEMIBL_04135;FLEJOH_03643;FNLDAG_04203;FOMADB_04119;GKLDEJ_03127;HFPBEP_04085;HIHJDO_04320;HLEDKO_04122;ICLPCH_04098;IJKJHL_01948;ILFCIO_04171;IPDLAB_04141;JEBLOM_04183;JFHJPL_04086;JFNAAB_03020;JGDOPI_04214;KBDFIK_04128 | hypothetical protein | |||
| 89 | group_3103 | gene_presence_absence | PE_PGRS48-like (group_3103) | group_3103 | Rv2853 | low confidence | PE_PGRS48 | PE-PGRS family protein PE_PGRS48 | Rv2853 | PE_PGRS48 | PE-PGRS family protein PE_PGRS48 | low | 99.46 | 53.27 | Low-confidence GenBank rescue; treat as tentative and keep the Panaroo cluster ID. | identity=99.46; coverage=53.27 | 48 | 50 | 0.9600 | 43 | 50 | 0.8600 | Check manually | -7.3 | 3.34483 | 0.7548-14.82 | 0.754776 | 14.8228 | 0.000546 | 8.0047 | Panaroo/Bakta+GenBank | nucleotide_similarity | 3162268..3164115 | matched_representative_sequence=group_3103 | AEDLOG_03361;AEMPHK_03156;AFKOAF_03680;AFNKCG_02276;AFNKCG_02450;ANMCAC_03258;APAKNA_01881;BDILPO_02972;BDMCKA_03815;BGEAED_01110;BHJHEC_03826;BKLOHC_04242;BPEJMN_03546;BPLIPK_03973;CBPCJH_00804;CIMEKD_02934;CKHCDK_03202;CKHCDK_03291;CKHCDK_04170;DBCCLE_03864;DJMHJN_02458;DNOEHN_02382;DOFGLF_03896;DPLIOB_02912;EBKMEK_00035;EEGMED_03049;EEGMED_03998;EEMIBL_02723;EOJHMN_03217;EPBFME_02245 | PE-PGRS family protein PE_PGRS48 | ||
| 90 | group_439 | gene_presence_absence | Rv1817 (group_439) | group_439 | Rv1817 | high confidence | group_439 | FAD-dependent oxidoreductase 2 FAD binding domain-containing protein | Rv1817 | flavoprotein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 49 | 50 | 0.9800 | 44 | 50 | 0.8800 | Check manually | -8.18 | 4.82022 | 0.7802-29.78 | 0.780225 | 29.7793 | 0.00187 | 7.9973 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 2059595..2061058 | matched_representative_sequence=group_439 | AEDLOG_03893;AEMPHK_01455;AFKOAF_01385;AFNKCG_03496;ANMCAC_01482;APAKNA_00960;BDILPO_01782;BDMCKA_02627;BGEAED_02389;BHJHEC_02883;BPEJMN_01721;BPLIPK_02933;CBPCJH_01386;CIMEKD_01172;CKHCDK_03808;DBCCLE_03566;DJMHJN_01262;DNOEHN_02631;DOFGLF_01366;DPLIOB_03818;EBKMEK_03827;EEGMED_03345;EEMIBL_02006;EOJHMN_03281;EPBFME_01281;FDDMPP_00974;FGOACM_03514;FLEJOH_03893;FNACPH_01545;FNLDAG_04131 | flavoprotein | |||
| 91 | group_1310 | gene_presence_absence | hycE | group_1310 | Rv0087 | high confidence | hycE | formate hydrogenase HycE | Rv0087 | hycE | formate hydrogenase HycE | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 42 | 50 | 0.8400 | 16 | 50 | 0.3200 | cases (rpoB 763031 T C present) | 1.36 | 10.4545 | 4.078-26.8 | 4.07751 | 26.805 | 0.0273 | 7.9499 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 95414..96892 | matched_representative_sequence=0_refound_93 | 0_refound_93;13_refound_582_pseudo;95_refound_2363_pseudo;AEDLOG_00570;AEMPHK_02223;AFNKCG_03438;ANMCAC_02597;APAKNA_00116;BGEAED_00385;BPEJMN_02951;CIMEKD_01991;DBCCLE_01453;DJMHJN_03458;DNOEHN_01838;DPLIOB_00726;EBKMEK_02321;EEMIBL_01559;EOJHMN_01523;EPBFME_02414;FDDMPP_03213;FLEJOH_00575;FNACPH_02596;GNKHBM_01027;HEJICF_02156;HLIGOK_00216;HNJHNP_02170;IDADDB_01002;IEDNOI_01940;IJGDKF_00789;IJKJHL_01716 | formate hydrogenase HycE | ||
| 92 | group_2820 | gene_presence_absence | PE_PGRS15-like | group_2820 | Rv0872c | medium confidence | PE_PGRS15 | hypothetical protein;PE family protein | Rv0872c | PE_PGRS15 | PE-PGRS family protein PE_PGRS15 | medium | 99.70 | 72.95 | Medium-confidence GenBank rescue; inspect manually before biological interpretation. | identity=99.70; coverage=72.95 | 48 | 50 | 0.9600 | 41 | 50 | 0.8200 | Check manually | -7.27 | 4.44096 | 1.038-19 | 1.03803 | 18.9996 | 0.00177 | 7.9029 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(968424..970244) | matched_representative_sequence=group_2820 | 2_refound_190_pseudo;38_refound_1084_pseudo;AEDLOG_00946;AEMPHK_00688;AFKOAF_03749;AFNKCG_01862;ANMCAC_01267;APAKNA_02425;BDILPO_01923;BDMCKA_03399;BGEAED_04029;BHJHEC_01555;BKLOHC_03626;BPEJMN_00705;BPLIPK_00744;CBPCJH_03954;CIMEKD_00655;CKHCDK_04086;DBCCLE_00764;DJMHJN_00449;DNOEHN_02071;DOFGLF_03957;DPLIOB_03999;EBKMEK_00818;EEGMED_04099;EEMIBL_01802;EOJHMN_03870;EPBFME_01448;FDDMPP_00913;FGOACM_02884 | PE-PGRS family protein PE_PGRS15 | ||
| 93 | group_1398 | gene_presence_absence | group_1398 | group_1398 | Rv3851 | none confidence | group_1398 | membrane protein | Rv3851 | membrane protein | none | 42.61 | 5.05 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=42.61; coverage=5.05 | 2 | 50 | 0.0400 | 9 | 50 | 0.1800 | Check manually | 7.27 | 0.225176 | 0.05263-0.9634 | 0.0526327 | 0.963363 | 0.00177 | 7.9029 | Panaroo/Bakta+GenBank | nucleotide_similarity | 4324683..4324967 | matched_representative_sequence=group_1398 | 12_refound_494_pseudo;22_refound_887_pseudo;40_refound_1246_pseudo;94_refound_2274_pseudo;FOMADB_03732;JEBLOM_02486;LFDDMP_03233;LPCJNG_03580;NJPOJP_02993;NNCHJK_03087;ODNJBD_02712 | membrane protein | |||
| 94 | group_864 | gene_presence_absence | group_864 | group_864 | Rv2957 | none confidence | group_864 | PGL/p-HBAD biosynthesis glycosyltransferase | Rv2957 | PGL/p-HBAD biosynthesis glycosyltransferase | none | 14.26 | 2.33 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=14.26; coverage=2.33 | 2 | 50 | 0.0400 | 8 | 50 | 0.1600 | Check manually | 7.79 | 0.257732 | 0.05931-1.12 | 0.0593138 | 1.1199 | 0.00116 | 7.8916 | Panaroo/Bakta+GenBank | nucleotide_similarity | 3309470..3310297 | matched_representative_sequence=group_864 | HFPBEP_03600;HIHJDO_03233;JEBLOM_02307;KBDFIK_03272;LFDDMP_02033;LPCJNG_02572;NJPOJP_03500;NNCHJK_03614;ODNJBD_02620;OJHMIJ_03561 | PGL/p-HBAD biosynthesis glycosyltransferase | |||
| 95 | group_632 | gene_presence_absence | idsA2 | group_632 | Rv2173 | none confidence | idsA2 | geranylgeranyl pyrophosphate synthetase IdsA | Rv2173 | idsA2 | geranylgeranyl pyrophosphate synthetase IdsA | none | 38.11 | 2.53 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=38.11; coverage=2.53 | 2 | 50 | 0.0400 | 8 | 50 | 0.1600 | Check manually | 7.79 | 0.257732 | 0.05931-1.12 | 0.0593138 | 1.1199 | 0.00116 | 7.8916 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2434847..2435905 | matched_representative_sequence=group_632 | BKLOHC_01290;HFPBEP_01829;HIHJDO_02819;JEBLOM_01658;LFDDMP_01228;LPCJNG_00933;NJPOJP_02479;NNCHJK_01832;ODNJBD_00907;OJHMIJ_02589 | geranylgeranyl pyrophosphate synthetase IdsA | ||
| 96 | group_3067 | gene_presence_absence | PE_PGRS33-like (group_3067) | group_3067 | Rv1818c | low confidence | PE_PGRS33 | PE-PGRS family protein PE_PGRS33 | Rv1818c | PE_PGRS33 | PE-PGRS family protein PE_PGRS33 | low | 99.63 | 47.54 | Low-confidence GenBank rescue; treat as tentative and keep the Panaroo cluster ID. | identity=99.63; coverage=47.54 | 46 | 50 | 0.9200 | 39 | 50 | 0.7800 | Check manually | -5.08 | 3.00844 | 0.9342-9.688 | 0.934234 | 9.68783 | 0.000518 | 7.8747 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(2061178..2062674) | matched_representative_sequence=group_3067 | 19_refound_796_pseudo;1_refound_173_pseudo;2_refound_195_pseudo;36_refound_1057_pseudo;38_refound_1088_pseudo;42_refound_1365_pseudo;62_refound_1732_pseudo;64_refound_1783_pseudo;67_refound_1823_pseudo;82_refound_2098_pseudo;91_refound_2220_pseudo;92_refound_2240_pseudo;AEDLOG_03892;AEMPHK_01454;AFKOAF_01386;ANMCAC_01481;APAKNA_00959;BDILPO_01781;BDMCKA_02626;BGEAED_02388;BPEJMN_01720;BPLIPK_02932;CBPCJH_01385;CIMEKD_01171;CKHCDK_03807;DJMHJN_01263;DOFGLF_01367;DPLIOB_03817;EEGMED_03344;EEMIBL_02005 | PE-PGRS family protein PE_PGRS33 | ||
| 97 | group_3435 | gene_presence_absence | group_3435 | group_3435 | Rv1580c | none confidence | group_3435 | phage protein | Rv1580c | phage protein | none | 39.63 | 3.16 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=39.63; coverage=3.16 | 1 | 50 | 0.0200 | 6 | 50 | 0.1200 | Check manually | 7.29 | 0.207459 | 0.03358-1.282 | 0.0335803 | 1.28168 | 0.00278 | 7.8251 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(1783620..1783892) | matched_representative_sequence=group_3435 | BKLOHC_04166;HFPBEP_04147;LPCJNG_04155;NJPOJP_04104;NNCHJK_04150;ODNJBD_04145;OJHMIJ_04122 | phage protein | |||
| 98 | group_3093 | gene_presence_absence | PE_PGRS2 | group_3093 | Rv0124 | high confidence | PE_PGRS2 | hypothetical protein;PE domain-containing protein | Rv0124 | PE_PGRS2 | PE-PGRS family protein PE_PGRS2 | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 41 | 50 | 0.8200 | 32 | 50 | 0.6400 | Check manually | -3.38 | 2.48664 | 1.004-6.16 | 1.00385 | 6.15964 | 0.000313 | 7.8187 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 149533..150996 | matched_representative_sequence=37_refound_1068 | 14_refound_636_pseudo;2_refound_196_pseudo;36_refound_1059_pseudo;37_refound_1068;38_refound_1089;42_refound_1366_pseudo;45_refound_1482;69_refound_1862;96_refound_2424_pseudo;AEMPHK_00484;AFKOAF_02199;ANMCAC_00464;APAKNA_00081;BDILPO_00218;BGEAED_01716;BHJHEC_01182;BPEJMN_00221;BPLIPK_00705;CBPCJH_02271;CIMEKD_00164;DJMHJN_00163;DNOEHN_00567;DOFGLF_00031;EBKMEK_00371;EEGMED_03136;EEMIBL_00748;EOJHMN_03473;EPBFME_00425;FDDMPP_00223;FGOACM_01327 | PE-PGRS family protein PE_PGRS2 | ||
| 99 | group_857 | gene_presence_absence | group_857 | group_857 | Rv0371c | none confidence | group_857 | hypothetical protein | Rv0371c | hypothetical protein | none | 18.44 | 3.12 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=18.44; coverage=3.12 | 1 | 50 | 0.0200 | 11 | 50 | 0.2200 | Check manually | 4.57 | 0.104084 | 0.01805-0.6002 | 0.0180485 | 0.600245 | 0.0308 | 7.7756 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(448040..448633) | matched_representative_sequence=group_857 | BKLOHC_04041;FNLDAG_03841;FOMADB_04073;HFPBEP_04093;JEBLOM_03871;LFDDMP_03768;LPCJNG_03949;NGOKMK_03215;NJPOJP_04051;NNCHJK_04103;ODNJBD_03930;OJHMIJ_04053 | hypothetical protein | |||
| 100 | group_301 | gene_presence_absence | rpsT | group_301 | Rv2412 | high confidence | rpsT | 30S ribosomal protein S20 | Rv2412 | rpsT | 30S ribosomal protein S20 | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 1 | 50 | 0.0200 | 11 | 50 | 0.2200 | Check manually | 4.57 | 0.104084 | 0.01805-0.6002 | 0.0180485 | 0.600245 | 0.0308 | 7.7756 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 2710075..2710335 | matched_representative_sequence=group_3011 | BKLOHC_04040;FNLDAG_03840;FOMADB_04074;HFPBEP_04092;JEBLOM_03872;LFDDMP_03769;LPCJNG_03950;NGOKMK_03214;NJPOJP_04052;NNCHJK_04102;ODNJBD_03929;OJHMIJ_04054 | 30S ribosomal protein S20 |
Showing 100 of 100 rows.
| rank | feature id | feature type | display name | display label | gene name | product | reference locus tag | reference gene | reference product | annotation confidence | reference identity | reference coverage | interpretation note | annotation evidence | case (rpoB 763031 T C present) present | case (rpoB 763031 T C present) total | case (rpoB 763031 T C present) frequency | control (rpoB 763031 T C absent) present | control (rpoB 763031 T C absent) total | control (rpoB 763031 T C absent) frequency | enriched in | beta | odds ratio | odds ratio ci95 | odds ratio ci95 lower | odds ratio ci95 upper | pyseer pvalue | q value | priority score | annotation source | reference match type | reference location | annotation note | cluster member ids | notes | display product |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | group_2286 | gene_presence_absence | rplW | group_2286 | Rv0703 | none confidence | rplW | 50S ribosomal protein L23 | Rv0703 | rplW | 50S ribosomal protein L23 | none | 21.83 | 1.93 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=21.83; coverage=1.93 | 1 | 50 | 0.0200 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -7.78 | 0.00030003 | 1.193e-05-0.007544 | 1.19329e-05 | 0.00754369 | 3.56e-16 | 30.1512 | Panaroo/Bakta+GenBank | nucleotide_similarity | 802133..802435 | matched_representative_sequence=group_2286 | AEDLOG_01250;AFKOAF_02797;APAKNA_00381;BDILPO_00329;BDMCKA_00770;BGEAED_00081;BHJHEC_01439;BKLOHC_00975;BPLIPK_01269;CBPCJH_00995;DOFGLF_01828;DPLIOB_00501;EEGMED_02335;EEMIBL_01291;FGOACM_00119;FLEJOH_01885;FNLDAG_02828;FOMADB_00225;GAGFCG_00499;GKEIOM_01002;GKLDEJ_00380;HBIPEG_01813;HFAJAL_00718;HFPBEP_02167;HIHJDO_03875;HLEDKO_00971;IJGDKF_00488;ILFCIO_01192;IOJEPD_00265;IPDLAB_00716 | 50S ribosomal protein L23 | ||
| 2 | group_3150 | gene_presence_absence | ccdA | group_3150 | Rv0527 | none confidence | ccdA | cytochrome C-type biogenesis protein CcdA | Rv0527 | ccdA | cytochrome C-type biogenesis protein CcdA | none | 36.55 | 2.47 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=36.55; coverage=2.47 | 49 | 50 | 0.9800 | 1 | 50 | 0.0200 | cases (rpoB 763031 T C present) | 8.78 | 1089 | 109.5-1.083e+04 | 109.483 | 10832 | 3.46e-16 | 28.5497 | Panaroo/Bakta+GenBank | nucleotide_similarity | 617493..618272 | matched_representative_sequence=group_3150 | AEMPHK_02800;AEMPHK_02801;AFNKCG_02062;AFNKCG_02063;ANMCAC_03049;ANMCAC_03050;BHJHEC_04034;BHJHEC_04035;BPEJMN_02687;BPEJMN_02688;CIMEKD_02693;CIMEKD_02694;CKHCDK_01640;DBCCLE_02628;DBCCLE_02629;DJMHJN_03235;DJMHJN_03236;DNOEHN_01662;DNOEHN_01663;EBKMEK_02740;EBKMEK_02741;EOJHMN_01713;EOJHMN_01714;EPBFME_02959;EPBFME_02960;FDDMPP_03885;FDDMPP_03886;FNACPH_03144;FNACPH_03145;GNKHBM_02961 | cytochrome C-type biogenesis protein CcdA | ||
| 3 | group_2789 | gene_presence_absence | cyp144 | group_2789 | Rv1777 | none confidence | cyp144 | cytochrome P450 Cyp144 | Rv1777 | cyp144 | cytochrome P450 Cyp144 | none | 18.31 | 6.09 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=18.31; coverage=6.09 | 49 | 50 | 0.9800 | 1 | 50 | 0.0200 | cases (rpoB 763031 T C present) | 8.78 | 1089 | 109.5-1.083e+04 | 109.483 | 10832 | 3.46e-16 | 28.5497 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2010656..2011960 | matched_representative_sequence=group_2789 | AEMPHK_02802;AFNKCG_02064;ANMCAC_03051;BHJHEC_04033;BPEJMN_02689;CIMEKD_02695;CKHCDK_01642;DBCCLE_02627;DJMHJN_03234;DNOEHN_01664;EBKMEK_02739;EOJHMN_01712;EPBFME_02961;FDDMPP_03887;FNACPH_03146;GNKHBM_02963;HEJICF_02747;HIHJDO_00196;HLIGOK_02329;HNJHNP_02577;ICLPCH_01675;IDADDB_02773;IEDNOI_02333;IJKJHL_01495;ILDPAE_03117;IMGGMF_01607;INBOBH_02518;JGDOPI_03074;JGFCNM_03002;JIEBBG_02335 | cytochrome P450 Cyp144 | ||
| 4 | group_2968 | gene_presence_absence | nmtR | group_2968 | Rv3744 | none confidence | nmtR | hypothetical protein;PknH-like extracellular domain-containing protein | Rv3744 | nmtR | HTH-type transcriptional regulator NmtR | none | 30.27 | 2.28 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=30.27; coverage=2.28 | 48 | 50 | 0.9600 | 1 | 50 | 0.0200 | cases (rpoB 763031 T C present) | 7.8 | 640.2 | 81.38-5036 | 81.3801 | 5036.32 | 6.25e-15 | 26.5265 | Panaroo/Bakta+GenBank | nucleotide_similarity | 4195440..4195802 | matched_representative_sequence=group_2968 | AEMPHK_02798;AFNKCG_02060;ANMCAC_03047;BHJHEC_04037;BPEJMN_02685;CIMEKD_02691;CKHCDK_01638;DBCCLE_02631;DJMHJN_03238;DNOEHN_01660;EBKMEK_02743;EOJHMN_01716;EPBFME_02957;FDDMPP_03883;FNACPH_03142;GNKHBM_02959;HEJICF_02743;HIHJDO_00193;HLIGOK_02333;HNJHNP_02573;ICLPCH_01672;IDADDB_02769;IEDNOI_02337;IJKJHL_01491;ILDPAE_03121;IMGGMF_01603;INBOBH_02522;JGDOPI_03078;JGFCNM_03006;KBONAM_02586 | HTH-type transcriptional regulator NmtR | ||
| 5 | group_1329 | gene_presence_absence | group_1329 | group_1329 | Rv2620c | none confidence | group_1329 | PknH-like extracellular domain-containing protein | Rv2620c | transmembrane protein | none | 40.71 | 1.86 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=40.71; coverage=1.86 | 48 | 50 | 0.9600 | 1 | 50 | 0.0200 | cases (rpoB 763031 T C present) | 7.8 | 640.2 | 81.38-5036 | 81.3801 | 5036.32 | 6.25e-15 | 26.5265 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(2947462..2947887) | matched_representative_sequence=group_1329 | AEMPHK_02799;AFNKCG_02061;ANMCAC_03048;BHJHEC_04036;BPEJMN_02686;CIMEKD_02692;CKHCDK_01639;DBCCLE_02630;DJMHJN_03237;DNOEHN_01661;EBKMEK_02742;EOJHMN_01715;EPBFME_02958;FDDMPP_03884;FNACPH_03143;GNKHBM_02960;HEJICF_02744;HIHJDO_00194;HLIGOK_02332;HNJHNP_02574;ICLPCH_01673;IDADDB_02770;IEDNOI_02336;IJKJHL_01492;ILDPAE_03120;IMGGMF_01604;INBOBH_02521;JGDOPI_03077;JGFCNM_03005;KBONAM_02587 | transmembrane protein | |||
| 6 | group_2915 | gene_presence_absence | dnaK | group_2915 | Rv0350 | none confidence | dnaK | Translation elongation factor EFTu-like domain-containing protein | Rv0350 | dnaK | chaperone protein DnaK | none | 11.36 | 5.56 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=11.36; coverage=5.56 | 46 | 50 | 0.9200 | 1 | 50 | 0.0200 | cases (rpoB 763031 T C present) | 6.26 | 341 | 51.48-2259 | 51.4763 | 2258.92 | 1.12e-11 | 22.3644 | Panaroo/Bakta+GenBank | nucleotide_similarity | 419835..421712 | matched_representative_sequence=group_2915 | AEMPHK_02797;AFNKCG_02059;ANMCAC_03046;BHJHEC_04038;BPEJMN_02684;CKHCDK_01637;DBCCLE_02632;DJMHJN_03239;DNOEHN_01659;EBKMEK_02744;EOJHMN_01717;EPBFME_02956;FDDMPP_03882;FNACPH_03141;GNKHBM_02958;HEJICF_02742;HIHJDO_00192;HLIGOK_02334;HNJHNP_02572;ICLPCH_01671;IDADDB_02768;IEDNOI_02338;IJKJHL_01490;ILDPAE_03122;IMGGMF_01602;INBOBH_02523;JGDOPI_03079;JGFCNM_03007;KBONAM_02585;LABCDH_03046 | chaperone protein DnaK | ||
| 7 | group_161 | gene_presence_absence | vapC13 | group_161 | Rv1838c | high confidence | vapC13 | ribonuclease VapC13 | Rv1838c | vapC13 | ribonuclease VapC13 | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 46 | 50 | 0.9200 | 1 | 50 | 0.0200 | cases (rpoB 763031 T C present) | 6.26 | 341 | 51.48-2259 | 51.4763 | 2258.92 | 1.12e-11 | 22.3644 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(2087257..2087652) | matched_representative_sequence=group_1612 | 17_refound_723_pseudo;AEMPHK_02796;AFNKCG_02058;ANMCAC_03045;BHJHEC_04039;BPEJMN_02683;CKHCDK_01636;DBCCLE_02633;DJMHJN_03240;DNOEHN_01658;EBKMEK_02745;EOJHMN_01718;EPBFME_02955;FDDMPP_03881;FNACPH_03140;GNKHBM_02957;HEJICF_02741;HIHJDO_00191;HLIGOK_02335;HNJHNP_02571;ICLPCH_01670;IDADDB_02767;IEDNOI_02339;IJKJHL_01489;ILDPAE_03123;IMGGMF_01601;INBOBH_02524;JGDOPI_03080;JGFCNM_03008;KBONAM_02584 | ribonuclease VapC13 | ||
| 8 | group_2755 | gene_presence_absence | Rv3785-like (group_2755) | group_2755 | Rv3785 | low confidence | group_2755 | hypothetical protein | Rv3785 | hypothetical protein | low | 72.82 | 88.62 | Low-confidence locus-level GenBank rescue. | identity=72.82; coverage=88.62 | 44 | 50 | 0.8800 | 3 | 50 | 0.0600 | cases (rpoB 763031 T C present) | 5.41 | 92.9121 | 23.79-362.8 | 23.7925 | 362.831 | 3.29e-11 | 20.0206 | Panaroo/Bakta+GenBank | nucleotide_similarity | 4231320..4232393 | matched_representative_sequence=group_2755 | AEMPHK_01496;AFNKCG_02801;ANMCAC_02133;BPEJMN_02072;CIMEKD_00431;DBCCLE_02436;DJMHJN_01642;DNOEHN_01387;EBKMEK_01641;EOJHMN_00730;EPBFME_01975;FDDMPP_02356;FNACPH_02067;GKLDEJ_02727;GNKHBM_01779;HEJICF_00699;HFAJAL_00786;HLIGOK_01549;HNJHNP_01531;IDADDB_01398;IEDNOI_01429;IJKJHL_01789;ILDPAE_01809;IMGGMF_01300;INBOBH_01400;JFNAAB_02666;JGDOPI_01970;JGFCNM_02208;JIEBBG_02313;KBONAM_00870 | hypothetical protein | |||
| 9 | group_2940 | gene_presence_absence | Rv0072 (group_2940) | group_2940 | Rv0072 | high confidence | group_2940 | hypothetical protein;Uncharacterized ABC transporter permease Rv0072 | Rv0072 | glutamine ABC transporter permease | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 14 | 50 | 0.2800 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -7.21 | 0.00393327 | 0.0002272-0.06808 | 0.00022724 | 0.0680806 | 9.95e-08 | 17.9922 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 80624..81673 | matched_representative_sequence=group_2940 | AEDLOG_00549;AFKOAF_01003;AFNKCG_04006;APAKNA_00137;BDILPO_03208;BDILPO_03943;BDMCKA_01131;BGEAED_00406;BHJHEC_00672;BKLOHC_00643;BPLIPK_00383;CBPCJH_00606;CKHCDK_02351;DOFGLF_03651;DPLIOB_00705;EEGMED_00127;EEMIBL_01538;FDDMPP_03192;FGOACM_00552;FLEJOH_00554;FNLDAG_00651;FOMADB_00775;GAGFCG_00966;GKEIOM_02346;GKLDEJ_02611;HBIPEG_01035;HEJICF_02135;HFAJAL_00212;HFPBEP_02094;HIHJDO_03987 | glutamine ABC transporter permease | |||
| 10 | group_1076 | gene_presence_absence | Rv0073 (group_1076) | group_1076 | Rv0073 | high confidence | group_1076 | ABC transporter domain-containing protein;hypothetical protein;Uncharacterized ABC transporter ATP-binding protein Rv0073 | Rv0073 | glutamine ABC transporter ATP-binding protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 14 | 50 | 0.2800 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -7.21 | 0.00393327 | 0.0002272-0.06808 | 0.00022724 | 0.0680806 | 9.95e-08 | 17.9922 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 81676..82668 | matched_representative_sequence=group_1076 | AEDLOG_00550;AFKOAF_01004;AFNKCG_04007;APAKNA_00136;BDILPO_03942;BDMCKA_01132;BGEAED_00405;BHJHEC_00671;BKLOHC_00644;BPLIPK_00382;CBPCJH_00605;CKHCDK_02350;DOFGLF_03652;DPLIOB_00706;EEGMED_00126;EEMIBL_01539;FDDMPP_03193;FGOACM_00551;FLEJOH_00555;FNLDAG_00652;FOMADB_00774;GAGFCG_00967;GKEIOM_02344;GKEIOM_02345;GKLDEJ_02612;HBIPEG_01034;HEJICF_02136;HFAJAL_00213;HFPBEP_02093;HIHJDO_03988 | glutamine ABC transporter ATP-binding protein | |||
| 11 | group_2793 | gene_presence_absence | vapB17 | group_2793 | Rv2526 | high confidence | vapB17 | hypothetical protein;Putative antitoxin VapB17 | Rv2526 | vapB17 | antitoxin VapB17 | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 15 | 50 | 0.3000 | 48 | 50 | 0.9600 | controls (rpoB 763031 T C absent) | -8.36 | 0.0225062 | 0.005526-0.09166 | 0.00552644 | 0.0916554 | 4.45e-10 | 17.8252 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 2851091..2851318 | matched_representative_sequence=13_refound_614 | 0_refound_139_pseudo;13_refound_614;3_refound_310_pseudo;41_refound_1351;44_refound_1462_pseudo;95_refound_2398_pseudo;AEDLOG_02135;AFKOAF_02067;AFNKCG_01693;APAKNA_01180;BDILPO_02295;BDMCKA_03456;BGEAED_00726;BHJHEC_01984;BPLIPK_02171;CBPCJH_01673;CKHCDK_02633;DOFGLF_01063;DPLIOB_02775;EEGMED_02427;EEMIBL_02636;FDDMPP_01524;FGOACM_02375;FLEJOH_02998;FOMADB_02868;GAGFCG_02739;GKEIOM_02775;GKLDEJ_01940;HBIPEG_02183;HEJICF_02077 | antitoxin VapB17 | ||
| 12 | group_2962 | gene_presence_absence | PE_PGRS49-like (group_2962) | group_2962 | Rv3344c | low confidence | PE_PGRS49 | PE-PGRS family protein PE_PGRS49 | Rv3344c | PE_PGRS49 | PE-PGRS family protein PE_PGRS49 | low | 100.00 | 50.00 | Low-confidence GenBank rescue; treat as tentative and keep the Panaroo cluster ID. | identity=100.00; coverage=50.00 | 3 | 50 | 0.0600 | 29 | 50 | 0.5800 | controls (rpoB 763031 T C absent) | -4.39 | 0.0537021 | 0.01586-0.1818 | 0.0158611 | 0.181823 | 2.24e-09 | 15.8686 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(3736984..3738000) | matched_representative_sequence=group_2962 | AFKOAF_04101;APAKNA_04083;BDILPO_03516;BGEAED_03867;BGEAED_03868;CBPCJH_03768;CBPCJH_03769;DOFGLF_03839;EEGMED_03522;EEGMED_03523;EEMIBL_03822;EEMIBL_03823;FGOACM_03029;FLEJOH_04049;GAGFCG_03889;GKLDEJ_03872;HBIPEG_03846;HBIPEG_03847;HFAJAL_03963;HIHJDO_01905;IJGDKF_03790;IJGDKF_03791;ILFCIO_04100;IOJEPD_04096;IPDLAB_03880;JFNAAB_03083;KOLHLA_03646;KOLHLA_03647;LNDNPG_04035;MHDACH_03535 | PE-PGRS family protein PE_PGRS49 | ||
| 13 | group_3104 | gene_presence_absence | Rv2817c (group_3104) | group_3104 | Rv2817c | high confidence | group_3104 | hypothetical protein;CRISPR-associated endonuclease Cas1 | Rv2817c | CRISPR-associated endonuclease Cas1 | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 16 | 50 | 0.3200 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -6.53 | 0.00473526 | 0.0002748-0.08159 | 0.000274825 | 0.0815887 | 8.27e-06 | 15.8048 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(3123967..3124983) | matched_representative_sequence=group_3104 | AEDLOG_03397;AFKOAF_03866;AFNKCG_03654;APAKNA_01917;BDILPO_02936;BDMCKA_04006;BGEAED_01074;BHJHEC_03982;BKLOHC_01955;BPLIPK_03786;CBPCJH_00768;CKHCDK_03908;DBCCLE_04047;DOFGLF_04000;DPLIOB_03469;EEGMED_03865;EEMIBL_02759;FDDMPP_04032;FGOACM_03625;FLEJOH_00580;FNLDAG_03547;FOMADB_03903;GAGFCG_01313;GKEIOM_01271;GKLDEJ_03610;HBIPEG_00829;HEJICF_03824;HFAJAL_00244;HFPBEP_03209;HIHJDO_02730 | CRISPR-associated endonuclease Cas1 | |||
| 14 | group_2919 | gene_presence_absence | Rv2818c (group_2919) | group_2919 | Rv2818c | high confidence | group_2919 | hypothetical protein;CRISPR system endoribonuclease Csm6 | Rv2818c | CRISPR-associated protein Csm6 | high | 100.00 | 92.07 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=92.07 | 16 | 50 | 0.3200 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -6.53 | 0.00473526 | 0.0002748-0.08159 | 0.000274825 | 0.0815887 | 8.27e-06 | 15.8048 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(3124996..3126144) | matched_representative_sequence=group_2919 | AEDLOG_03396;AFKOAF_03867;AFNKCG_03655;APAKNA_01916;BDILPO_02937;BDMCKA_04005;BGEAED_01075;BHJHEC_03983;BKLOHC_01954;BPLIPK_03785;CBPCJH_00769;CKHCDK_03909;DBCCLE_03584;DOFGLF_03999;DPLIOB_03470;EEGMED_03866;EEMIBL_02758;FDDMPP_04031;FGOACM_03624;FLEJOH_00581;FNLDAG_03548;FOMADB_03902;GAGFCG_01312;GKEIOM_01272;GKLDEJ_03611;HBIPEG_00828;HEJICF_03825;HFAJAL_00245;HFPBEP_03210;HIHJDO_02731 | CRISPR-associated protein Csm6 | |||
| 15 | group_1498 | gene_presence_absence | lppA | group_1498 | Rv2543 | high confidence | lppA | lipoprotein LppA | Rv2543 | lppA | lipoprotein LppA | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 16 | 50 | 0.3200 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -6.53 | 0.00473526 | 0.0002748-0.08159 | 0.000274825 | 0.0815887 | 8.27e-06 | 15.8048 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 2866468..2867127 | matched_representative_sequence=group_1498 | 50_refound_1544_pseudo;AEDLOG_02118;AFKOAF_02050;AFNKCG_01711;APAKNA_01197;BDILPO_02277;BDMCKA_02893;BGEAED_00709;BHJHEC_01967;BKLOHC_03083;BPLIPK_02154;CBPCJH_01690;CKHCDK_02650;DBCCLE_01505;DOFGLF_01080;DPLIOB_02758;EEGMED_02444;EEMIBL_02619;FDDMPP_01507;FGOACM_02358;FLEJOH_02981;FNLDAG_03133;FOMADB_01728;GAGFCG_02756;GKEIOM_02758;GKLDEJ_01957;HBIPEG_02166;HEJICF_02094;HFAJAL_01119;HFPBEP_03679 | lipoprotein LppA | ||
| 16 | group_915 | gene_presence_absence | Rv2819c (group_915) | group_915 | Rv2819c | high confidence | group_915 | hypothetical protein;CRISPR system Cms protein Csm5 | Rv2819c | CRISPR type III-associated RAMP protein Csm5 | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 16 | 50 | 0.3200 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -6.53 | 0.00473526 | 0.0002748-0.08159 | 0.000274825 | 0.0815887 | 8.27e-06 | 15.8048 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(3126240..3127367) | matched_representative_sequence=group_915 | AEDLOG_03395;AFKOAF_03868;AFNKCG_03656;APAKNA_01915;BDILPO_02938;BDMCKA_04004;BGEAED_01076;BHJHEC_03984;BKLOHC_01953;BPLIPK_03784;CBPCJH_00770;CKHCDK_03910;DBCCLE_03585;DOFGLF_03998;DPLIOB_03471;EEGMED_03867;EEMIBL_02757;FDDMPP_04030;FGOACM_03623;FLEJOH_00582;FNLDAG_03549;FOMADB_03901;GAGFCG_01311;GKEIOM_01273;GKLDEJ_03612;HBIPEG_00827;HEJICF_03826;HFAJAL_00246;HFPBEP_03211;HIHJDO_02732 | CRISPR type III-associated RAMP protein Csm5 | |||
| 17 | group_3239 | gene_presence_absence | PPE67 | group_3239 | Rv3739c | high confidence | PPE67 | PPE family protein PPE67 | Rv3739c | PPE67 | PPE family protein PPE67 | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 36 | 50 | 0.7200 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -12.1 | 0.0249232 | 0.00144-0.4314 | 0.00143991 | 0.431393 | 1.48e-07 | 15.1561 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(4190284..4190517) | matched_representative_sequence=group_3239 | 81_refound_2035_pseudo;AEDLOG_01234;AEMPHK_01548;AFKOAF_01479;ANMCAC_02185;APAKNA_00365;BDILPO_00313;BDMCKA_00754;BGEAED_00065;BHJHEC_01455;BKLOHC_02036;BPEJMN_02124;BPLIPK_01285;CBPCJH_00979;CIMEKD_00483;DBCCLE_02384;DJMHJN_01694;DNOEHN_01335;DOFGLF_01844;DPLIOB_00485;EBKMEK_01589;EEGMED_02351;EEMIBL_01307;EOJHMN_00678;EPBFME_02028;FGOACM_00135;FLEJOH_01901;FNACPH_02119;FNLDAG_00495;FOMADB_00241 | PPE family protein PPE67 | ||
| 18 | group_897 | gene_presence_absence | mpt83 | group_897 | Rv2873 | none confidence | mpt83 | cell surface lipoprotein | Rv2873 | mpt83 | cell surface lipoprotein | none | 16.09 | 5.44 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=16.09; coverage=5.44 | 5 | 50 | 0.1000 | 43 | 50 | 0.8600 | controls (rpoB 763031 T C absent) | -3.3 | 0.0208412 | 0.006428-0.06757 | 0.00642849 | 0.0675674 | 5.54e-07 | 14.8409 | Panaroo/Bakta+GenBank | nucleotide_similarity | 3183905..3184567 | matched_representative_sequence=group_897 | 20_refound_835_pseudo;AEDLOG_01658;AFKOAF_01016;APAKNA_01389;BDILPO_02737;BGEAED_03378;BHJHEC_00399;BKLOHC_00365;BPLIPK_00110;CBPCJH_00913;CKHCDK_01352;DOFGLF_01788;EEGMED_01902;EEMIBL_02271;FGOACM_01579;FLEJOH_03462;FNLDAG_00136;FOMADB_00373;GAGFCG_03079;GKEIOM_00883;GKLDEJ_00243;HEJICF_01674;HFAJAL_00389;HFPBEP_00151;HLEDKO_00282;ICLPCH_02639;IJGDKF_00069;ILFCIO_00808;IOJEPD_03535;JEBLOM_00083 | cell surface lipoprotein | ||
| 19 | group_1075 | gene_presence_absence | Rv0071 (group_1075) | group_1075 | Rv0071 | high confidence | group_1075 | maturase | Rv0071 | maturase | high | 97.52 | 92.61 | High-confidence locus-level GenBank rescue. | identity=97.52; coverage=92.61 | 14 | 50 | 0.2800 | 49 | 50 | 0.9800 | controls (rpoB 763031 T C absent) | -5.65 | 0.0120382 | 0.002124-0.06822 | 0.00212437 | 0.0682168 | 2e-05 | 14.0752 | Panaroo/Bakta+GenBank | nucleotide_similarity | 79486..80193 | matched_representative_sequence=group_1075 | AEDLOG_00548;AFKOAF_01002;AFNKCG_03799;APAKNA_00138;BDILPO_03207;BDMCKA_01130;BGEAED_00407;BHJHEC_00673;BKLOHC_00642;BPLIPK_00384;CBPCJH_00607;CKHCDK_02352;DOFGLF_00812;DPLIOB_00704;EEGMED_00128;EEMIBL_01537;FDDMPP_03191;FGOACM_00553;FLEJOH_00553;FNLDAG_00650;FOMADB_00776;GAGFCG_00965;GKEIOM_02347;GKLDEJ_02610;HBIPEG_01036;HEJICF_02134;HFAJAL_00211;HFPBEP_02095;HIHJDO_03986;HLEDKO_00415 | maturase | |||
| 20 | group_2489 | gene_presence_absence | PPE46 | group_2489 | Rv3018c | none confidence | PPE46 | hypothetical protein;Uncharacterized PPE family protein PPE66 | Rv3018c | PPE46 | PPE family protein PPE46 | none | 60.60 | 1.95 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=60.60; coverage=1.95 | 39 | 50 | 0.7800 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -4.93 | 0.0340077 | 0.001944-0.595 | 0.00194385 | 0.594968 | 5.37e-06 | 13.1480 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(3376939..3378243) | matched_representative_sequence=group_2489 | AEDLOG_01235;AEMPHK_01549;AFKOAF_01480;ANMCAC_02186;APAKNA_00366;BDILPO_00314;BDMCKA_00755;BGEAED_00066;BHJHEC_01454;BKLOHC_02035;BPEJMN_02125;BPLIPK_01284;CBPCJH_00980;CIMEKD_00484;DJMHJN_01695;DNOEHN_01334;DOFGLF_01843;DPLIOB_00486;EBKMEK_01588;EEGMED_02350;EEMIBL_01306;EOJHMN_00677;EPBFME_02029;FGOACM_00134;FLEJOH_01900;FNACPH_02120;FNLDAG_00496;FOMADB_00240;GAGFCG_00484;GKEIOM_00988 | PPE family protein PPE46 | ||
| 21 | group_2067 | gene_presence_absence | Rv2816c (group_2067) | group_2067 | Rv2816c | high confidence | group_2067 | CRISPR-associated endoribonuclease Cas2 | Rv2816c | CRISPR-associated endoribonuclease Cas2 | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 16 | 50 | 0.3200 | 49 | 50 | 0.9800 | controls (rpoB 763031 T C absent) | -5.37 | 0.0144928 | 0.002577-0.08151 | 0.00257682 | 0.0815113 | 0.000476 | 12.4309 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(3123625..3123966) | matched_representative_sequence=group_2067 | AEDLOG_03398;AFKOAF_03865;AFNKCG_03653;APAKNA_01918;BDILPO_02935;BDMCKA_04007;BGEAED_01073;BHJHEC_03981;BKLOHC_01956;BPLIPK_03787;CBPCJH_00767;CKHCDK_03907;DBCCLE_04046;DPLIOB_03468;EEGMED_03864;EEMIBL_02760;FDDMPP_04033;FGOACM_03626;FLEJOH_00579;FNLDAG_03546;FOMADB_03904;GAGFCG_01314;GKEIOM_01270;GKLDEJ_03609;HBIPEG_00830;HEJICF_03823;HFAJAL_00243;HFPBEP_03208;HIHJDO_02729;HLEDKO_03904 | CRISPR-associated endoribonuclease Cas2 | |||
| 22 | group_1420 | gene_presence_absence | PPE53 | group_1420 | Rv3159c | none confidence | PPE53 | PPE family protein PPE53 | Rv3159c | PPE53 | PPE family protein PPE53 | none | 50.27 | 19.16 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=50.27; coverage=19.16 | 49 | 50 | 0.9800 | 13 | 50 | 0.2600 | cases (rpoB 763031 T C present) | 4.39 | 91.6667 | 16.1-522 | 16.0982 | 521.968 | 0.00137 | 12.3816 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(3527391..3529163) | matched_representative_sequence=group_1420 | AEMPHK_04108;AFNKCG_04190;ANMCAC_04061;APAKNA_03299;BHJHEC_02239;BKLOHC_02971;BPEJMN_03033;CIMEKD_04113;CKHCDK_01833;DJMHJN_00375;DNOEHN_02931;DPLIOB_00179;EBKMEK_02878;EEMIBL_00962;EOJHMN_04107;EPBFME_04097;FDDMPP_00689;FNACPH_04097;FNLDAG_04135;GNKHBM_03409;HEJICF_00856;HFPBEP_04071;HIHJDO_01098;HLIGOK_03233;HNJHNP_03351;ICLPCH_04120;IDADDB_01187;IEDNOI_02834;IJGDKF_03559;IJKJHL_02157 | PPE family protein PPE53 | ||
| 23 | group_2775 | gene_presence_absence | Rv3517 (group_2775) | group_2775 | Rv3517 | high confidence | group_2775 | hypothetical protein;DUF559 domain-containing protein | Rv3517 | hypothetical protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 41 | 50 | 0.8200 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -4.58 | 0.0432517 | 0.002444-0.7654 | 0.00244409 | 0.765401 | 7.39e-05 | 11.6625 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 3953431..3954270 | matched_representative_sequence=group_2775 | AEDLOG_01777;AEMPHK_02125;AFKOAF_01295;ANMCAC_01695;APAKNA_02845;BDILPO_02516;BDMCKA_02076;BGEAED_02063;BHJHEC_02004;BKLOHC_00818;BPEJMN_01902;BPLIPK_02356;CBPCJH_02365;CIMEKD_01985;DBCCLE_01783;DJMHJN_02721;DNOEHN_01515;DOFGLF_02498;DPLIOB_02072;EBKMEK_01275;EEGMED_00992;EEMIBL_02765;EOJHMN_01771;EPBFME_01227;FGOACM_01797;FLEJOH_01627;FNACPH_01434;FNLDAG_02689;FOMADB_03282;GAGFCG_02624 | hypothetical protein | |||
| 24 | group_1439 | gene_presence_absence | PPE15 | group_1439 | Rv1039c | none confidence | PPE15 | Sulfite oxidase-like oxidoreductase | Rv1039c | PPE15 | PPE family protein PPE15 | none | 35.79 | 1.45 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=35.79; coverage=1.45 | 6 | 50 | 0.1200 | 32 | 50 | 0.6400 | controls (rpoB 763031 T C absent) | -2.98 | 0.0831461 | 0.03054-0.2264 | 0.0305389 | 0.226376 | 1.25e-05 | 11.4913 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(1161297..1162472) | matched_representative_sequence=group_1439 | AEDLOG_04067;APAKNA_04002;BDMCKA_04010;BKLOHC_02716;BPLIPK_04023;CKHCDK_04015;DPLIOB_04003;EEGMED_03831;EEMIBL_04057;FGOACM_03981;FLEJOH_03959;FNLDAG_03780;GAGFCG_04059;GKEIOM_04023;HFPBEP_03199;HIHJDO_02936;ICLPCH_03556;IJGDKF_04004;ILFCIO_03927;IOJEPD_01115;IPDLAB_02369;JEBLOM_02250;JFHJPL_04050;JFNAAB_03925;KBDFIK_00696;LFDDMP_01570;LNDNPG_04016;MHDACH_03936;NEGAKJ_03902;NEKGNJ_04013 | PPE family protein PPE15 | ||
| 25 | group_747 | gene_presence_absence | group_747 | group_747 | Rv2618 | none confidence | group_747 | hypothetical protein;GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol dimannoside mannosyltransferase | Rv2618 | hypothetical protein | none | 29.50 | 1.31 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=29.50; coverage=1.31 | 6 | 50 | 0.1200 | 32 | 50 | 0.6400 | controls (rpoB 763031 T C absent) | -2.98 | 0.0831461 | 0.03054-0.2264 | 0.0305389 | 0.226376 | 1.25e-05 | 11.4913 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2946434..2947111 | matched_representative_sequence=group_747 | AEDLOG_04068;APAKNA_04001;BDMCKA_04011;BKLOHC_02715;BPLIPK_04024;CKHCDK_04016;DPLIOB_04004;EEGMED_03830;EEMIBL_04058;FGOACM_03980;FLEJOH_03958;FNLDAG_03781;GAGFCG_04058;GKEIOM_04022;HFPBEP_03200;HIHJDO_02937;ICLPCH_03557;IJGDKF_04003;ILFCIO_03928;IOJEPD_01114;IPDLAB_02370;JEBLOM_02249;JFHJPL_04051;JFNAAB_03926;KBDFIK_00697;LFDDMP_01569;LNDNPG_04017;MHDACH_03935;NEGAKJ_03903;NEKGNJ_04012 | hypothetical protein | |||
| 26 | group_81 | gene_presence_absence | Rv2633c (group_81) | group_81 | Rv2633c | high confidence | group_81 | Membrane transport protein MMPL domain-containing protein | Rv2633c | hypothetical protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 6 | 50 | 0.1200 | 32 | 50 | 0.6400 | controls (rpoB 763031 T C absent) | -2.98 | 0.0831461 | 0.03054-0.2264 | 0.0305389 | 0.226376 | 1.25e-05 | 11.4913 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(2959335..2959820) | matched_representative_sequence=group_810 | AEDLOG_04066;APAKNA_04003;BDMCKA_04009;BKLOHC_02717;BPLIPK_04022;CKHCDK_04014;DPLIOB_04002;EEGMED_03832;EEMIBL_04056;FGOACM_03982;FLEJOH_03960;FNLDAG_03779;GAGFCG_04060;GKEIOM_04024;HFPBEP_03198;HIHJDO_02935;ICLPCH_03555;IJGDKF_04005;ILFCIO_03926;IOJEPD_01116;IPDLAB_02368;JEBLOM_02251;JFHJPL_04049;JFNAAB_03924;KBDFIK_00695;LFDDMP_01571;LNDNPG_04015;MHDACH_03937;NEGAKJ_03901;NEKGNJ_04014 | hypothetical protein | |||
| 27 | group_3019 | gene_presence_absence | group_3019 | group_3019 | Rv2509 | none confidence | group_3019 | short-chain type dehydrogenase/reductase | Rv2509 | short-chain type dehydrogenase/reductase | none | 20.60 | 6.13 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=20.60; coverage=6.13 | 13 | 50 | 0.2600 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 4.23 | 36.36 | 2.094-631.2 | 2.09447 | 631.209 | 0.00145 | 11.0229 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2824678..2825484 | matched_representative_sequence=group_3019 | 17_refound_732_pseudo;AEMPHK_04000;AFNKCG_03638;BPEJMN_04014;CIMEKD_04007;EOJHMN_03922;IDADDB_03510;IMGGMF_03898;JIEBBG_03604;LABCDH_03982;LEFJPD_04030;MILAMD_04001;NKKFEE_03972 | short-chain type dehydrogenase/reductase | |||
| 28 | group_3083 | gene_presence_absence | cut1 | group_3083 | Rv1758 | none confidence | cut1 | cutinase | Rv1758 | cut1 | cutinase | none | 40.36 | 6.20 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=40.36; coverage=6.20 | 8 | 50 | 0.1600 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 4.47 | 20.2 | 1.133-360.3 | 1.1325 | 360.299 | 0.000213 | 11.0079 | Panaroo/Bakta+GenBank | nucleotide_similarity | 1989042..1989566 | matched_representative_sequence=group_3083 | AFNKCG_02635;CKHCDK_00761;FDDMPP_02601;HEJICF_00438;HLIGOK_03797;JGDOPI_00546;OLKJCH_00838;ONNOIP_00679 | cutinase | ||
| 29 | group_1870 | gene_presence_absence | group_1870 | group_1870 | Rv1887 | none confidence | group_1870 | hypothetical protein | Rv1887 | hypothetical protein | none | 31.35 | 4.34 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=31.35; coverage=4.34 | 0 | 50 | 0.0000 | 14 | 50 | 0.2800 | controls (rpoB 763031 T C absent) | -3.05 | 0.0249232 | 0.00144-0.4314 | 0.00143991 | 0.431393 | 0.00214 | 10.9960 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2136258..2137400 | matched_representative_sequence=98_refound_2443 | 98_refound_2443;BDILPO_03794;DOFGLF_03843;EEMIBL_03964;FNLDAG_03973;HBIPEG_03779;HLEDKO_03235;IJGDKF_04064;ILFCIO_02348;IPDLAB_03823;NEKGNJ_03124;NFBOIH_03182;NJPOJP_01084;NOBKKO_03865 | hypothetical protein | |||
| 30 | group_2853 | gene_presence_absence | cut1 | group_2853 | Rv1758 | none confidence | cut1 | cutinase | Rv1758 | cut1 | cutinase | none | 30.00 | 6.27 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=30.00; coverage=6.27 | 12 | 50 | 0.2400 | 0 | 50 | 0.0000 | cases (rpoB 763031 T C present) | 4.23 | 32.7922 | 1.882-571.3 | 1.88232 | 571.28 | 0.00145 | 10.8739 | Panaroo/Bakta+GenBank | nucleotide_similarity | 1989042..1989566 | matched_representative_sequence=group_2853 | AEMPHK_04001;AFNKCG_03639;BPEJMN_04015;CIMEKD_04008;EOJHMN_03921;IDADDB_03509;IMGGMF_03899;JIEBBG_03605;LABCDH_03983;LEFJPD_04029;MILAMD_04002;NKKFEE_03971 | cutinase | ||
| 31 | group_3121 | gene_presence_absence | PE_PGRS46 | group_3121 | Rv2634c | high confidence | PE_PGRS46 | PE-PGRS family protein PE_PGRS46 | Rv2634c | PE_PGRS46 | PE-PGRS family protein PE_PGRS46 | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 41 | 50 | 0.8200 | 45 | 50 | 0.9000 | controls (rpoB 763031 T C absent) | -6.86 | 0.528051 | 0.1704-1.637 | 0.170356 | 1.6368 | 1.32e-07 | 10.8007 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(2960105..2962441) | matched_representative_sequence=3_refound_326 | 12_refound_514;22_refound_891;3_refound_326;44_refound_1470;80_refound_2031_pseudo;94_refound_2299_pseudo;95_refound_2415;AEDLOG_03226;AEDLOG_03227;AEMPHK_03523;AFKOAF_02598;ANMCAC_01892;APAKNA_01292;BDILPO_03745;BDMCKA_03635;BGEAED_03796;BHJHEC_03641;BPEJMN_01212;BPLIPK_03075;CBPCJH_03618;CIMEKD_03588;CKHCDK_03775;DBCCLE_03633;DJMHJN_01401;DNOEHN_03550;DOFGLF_03351;DPLIOB_01887;EBKMEK_03896;EEGMED_01325;EEMIBL_03901 | PE-PGRS family protein PE_PGRS46 | ||
| 32 | group_3313 | gene_presence_absence | Rv3113 (group_3313) | group_3313 | Rv3113 | high confidence | group_3313 | phosphatase | Rv3113 | phosphatase | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 0 | 50 | 0.0000 | 19 | 50 | 0.3800 | controls (rpoB 763031 T C absent) | -2.64 | 0.0159939 | 0.0009324-0.2744 | 0.00093238 | 0.274357 | 0.0188 | 10.6922 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 3480074..3480742 | matched_representative_sequence=group_3313 | AFKOAF_04135;BDILPO_04095;BDMCKA_04098;BHJHEC_04103;BKLOHC_04148;CBPCJH_04104;DOFGLF_04088;FOMADB_04093;HBIPEG_04109;HLEDKO_04097;ILFCIO_04154;JEBLOM_04058;KBDFIK_03598;LFDDMP_04005;NJPOJP_04096;NMJEMD_04114;ODHDPD_04117;OJHMIJ_04115;PMNAOE_04115 | phosphatase | |||
| 33 | group_3127 | gene_presence_absence | group_3127 | group_3127 | no_reference_locus | none confidence | group_3127 | hypothetical protein;PPE family domain-containing protein | none | No confident reference gene assignment; report the stable Panaroo cluster ID. | no sequence identity/coverage evidence available | 12 | 50 | 0.2400 | 37 | 50 | 0.7400 | controls (rpoB 763031 T C absent) | -2.75 | 0.116883 | 0.04794-0.2849 | 0.0479444 | 0.284948 | 3.26e-05 | 10.5836 | Panaroo/Bakta | none | No confident GenBank reference match found. The cluster may be accessory, divergent, absent from the reference, or not represented in Panaroo sequence outputs. | 11_refound_473_pseudo;14_refound_637_pseudo;20_refound_856_pseudo;28_refound_951_pseudo;36_refound_1060_pseudo;38_refound_1090_pseudo;42_refound_1368_pseudo;51_refound_1560_pseudo;70_refound_1889_pseudo;73_refound_1921_pseudo;8_refound_427_pseudo;98_refound_2452_pseudo;99_refound_2465_pseudo;9_refound_443_pseudo;AEDLOG_02950;AFKOAF_00688;BGEAED_04077;BKLOHC_03755;BKLOHC_03756;CBPCJH_03005;CKHCDK_03361;DOFGLF_03971;DPLIOB_03500;EEGMED_00456;FDDMPP_02446;FGOACM_02056;GKEIOM_01268;HBIPEG_04064;HFAJAL_03275;HFPBEP_00012 | hypothetical protein;PPE family domain-containing protein | ||||||||
| 34 | group_3140 | gene_presence_absence | PE_PGRS43-like | group_3140 | Rv2490c | medium confidence | PE_PGRS43 | hypothetical protein;PE family protein | Rv2490c | PE_PGRS43 | PE-PGRS family protein PE_PGRS43 | medium | 99.21 | 71.37 | Medium-confidence GenBank rescue; inspect manually before biological interpretation. | identity=99.21; coverage=71.37 | 47 | 50 | 0.9400 | 40 | 50 | 0.8000 | Check manually | -8.82 | 3.51852 | 0.978-12.66 | 0.977975 | 12.6588 | 3.07e-06 | 10.3278 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(2801254..2806236) | matched_representative_sequence=group_3140 | AEDLOG_01526;AEDLOG_03776;AEDLOG_03777;AEDLOG_03778;AEDLOG_03779;AEMPHK_01973;AFKOAF_03100;AFKOAF_03101;AFKOAF_03391;AFNKCG_03262;AFNKCG_03263;AFNKCG_03264;AFNKCG_04058;ANMCAC_01071;APAKNA_00521;BDILPO_00943;BDMCKA_03594;BDMCKA_03595;BDMCKA_04013;BDMCKA_04103;BGEAED_02661;BHJHEC_02213;BHJHEC_02214;BHJHEC_03535;BHJHEC_03536;BPEJMN_01744;BPLIPK_01827;BPLIPK_03788;BPLIPK_03789;BPLIPK_04117 | PE-PGRS family protein PE_PGRS43 | ||
| 35 | group_3101 | gene_presence_absence | PE_PGRS4 | group_3101 | Rv0279c | none confidence | PE_PGRS4 | PE-PGRS family protein PE_PGRS4 | Rv0279c | PE_PGRS4 | PE-PGRS family protein PE_PGRS4 | none | 86.75 | 35.59 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=86.75; coverage=35.59 | 8 | 50 | 0.1600 | 25 | 50 | 0.5000 | controls (rpoB 763031 T C absent) | -2.77 | 0.2 | 0.07982-0.5011 | 0.0798233 | 0.501107 | 1.71e-05 | 10.0889 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(336560..339073) | matched_representative_sequence=5_refound_372 | 5_refound_372;AEDLOG_04138;AFKOAF_03643;AFNKCG_03875;APAKNA_03324;BDILPO_00057;BDMCKA_04054;BGEAED_04103;CBPCJH_04089;CKHCDK_04177;DOFGLF_02700;DPLIOB_04133;EEGMED_03291;FDDMPP_00057;FGOACM_04108;HBIPEG_00436;HFAJAL_04078;HIHJDO_04163;ICLPCH_04099;IDADDB_01434;IJGDKF_04103;IPDLAB_04118;JFHJPL_04119;KOLHLA_04104;LNDNPG_00058;MLLPLE_04046;NEKGNJ_03310;NFBOIH_04119;NMJEMD_02408;NOBKKO_04100 | PE-PGRS family protein PE_PGRS4 | ||
| 36 | group_2997 | gene_presence_absence | PPE34 | group_2997 | Rv1917c | none confidence | PPE34 | hypothetical protein;PPE family protein | Rv1917c | PPE34 | PPE family protein PPE34 | none | 94.64 | 39.68 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=94.64; coverage=39.68 | 49 | 50 | 0.9800 | 32 | 50 | 0.6400 | cases (rpoB 763031 T C present) | 2.63 | 18.7846 | 3.358-105.1 | 3.3577 | 105.09 | 0.00218 | 9.8930 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(2162932..2167311) | matched_representative_sequence=group_2997 | AEDLOG_01782;AEDLOG_03752;AEMPHK_03652;AEMPHK_03653;AFKOAF_01213;AFNKCG_02248;AFNKCG_03014;ANMCAC_01407;BDILPO_01674;BDILPO_03793;BDMCKA_01710;BHJHEC_02941;BKLOHC_00410;BPEJMN_03739;CIMEKD_01066;CIMEKD_03641;CIMEKD_04109;CKHCDK_03141;CKHCDK_03546;DBCCLE_03310;DBCCLE_04000;DBCCLE_04001;DJMHJN_01368;DJMHJN_03831;DJMHJN_04078;DNOEHN_01729;DNOEHN_01730;DOFGLF_01473;DOFGLF_03844;DPLIOB_03246 | PPE family protein PPE34 | ||
| 37 | group_3070 | gene_presence_absence | ;tnp | group_3070 | Rv1313c | high confidence | ;tnp | hypothetical protein;Transposase IS204/IS1001/IS1096/IS1165 DDE domain-containing protein;ISL3 family transposase;ISL3 family IS1557 transposase | Rv1313c | insertion sequence element IS1557 transposase | high | 100.00 | 100.00 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=100.00; coverage=100.00 | 44 | 50 | 0.8800 | 20 | 50 | 0.4000 | cases (rpoB 763031 T C present) | 2.18 | 10.1857 | 3.765-27.56 | 3.76464 | 27.5589 | 0.000471 | 9.6755 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(1468171..1469505) | matched_representative_sequence=group_3070 | AEMPHK_01614;AEMPHK_04123;AFNKCG_01057;ANMCAC_02367;ANMCAC_04075;BDMCKA_04088;BGEAED_03953;BKLOHC_00749;BKLOHC_01080;BPEJMN_01245;BPEJMN_04103;CIMEKD_04117;DBCCLE_04089;DJMHJN_01877;DJMHJN_04094;DNOEHN_03637;DNOEHN_04116;EBKMEK_01773;EBKMEK_04128;EEGMED_04171;EOJHMN_03529;EOJHMN_04130;EPBFME_02093;EPBFME_04106;FDDMPP_01665;FDDMPP_02341;FNACPH_02295;FNACPH_04107;FOMADB_04085;GAGFCG_04117 | insertion sequence element IS1557 transposase | |||
| 38 | group_3428 | gene_presence_absence | sppA | group_3428 | Rv0724 | none confidence | sppA | protease IV SppA | Rv0724 | sppA | protease IV SppA | none | 33.57 | 1.39 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=33.57; coverage=1.39 | 6 | 50 | 0.1200 | 30 | 50 | 0.6000 | controls (rpoB 763031 T C absent) | -2.18 | 0.0981765 | 0.03629-0.2656 | 0.036286 | 0.265629 | 0.000471 | 9.6755 | Panaroo/Bakta+GenBank | nucleotide_similarity | 815663..817534 | matched_representative_sequence=group_3428 | AEDLOG_04121;AFKOAF_04118;APAKNA_04093;BDILPO_04081;BHJHEC_04086;BPLIPK_04110;CBPCJH_04092;CKHCDK_04191;DOFGLF_04075;DPLIOB_04145;EEMIBL_04116;FGOACM_04123;FLEJOH_04130;FNLDAG_04156;GKLDEJ_04104;HBIPEG_04099;HEJICF_04146;HFAJAL_04083;HFPBEP_04114;HLEDKO_04087;HLIGOK_04125;IJGDKF_04108;IJKJHL_04167;IPDLAB_04124;JFHJPL_04101;JFNAAB_04128;JGDOPI_04190;LNDNPG_04116;NFBOIH_04156;NJPOJP_04078 | protease IV SppA | ||
| 39 | group_600 | gene_presence_absence | folP2 | group_600 | Rv1207 | none confidence | folP2 | dihydropteroate synthase | Rv1207 | folP2 | dihydropteroate synthase | none | 19.35 | 33.70 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=19.35; coverage=33.70 | 26 | 50 | 0.5200 | 43 | 50 | 0.8600 | controls (rpoB 763031 T C absent) | -3.67 | 0.186488 | 0.07213-0.4822 | 0.0721306 | 0.482152 | 5.79e-05 | 9.6602 | Panaroo/Bakta+GenBank | nucleotide_similarity | 1351191..1352147 | matched_representative_sequence=group_600 | AEDLOG_03546;AEMPHK_01725;AFKOAF_00426;APAKNA_02036;BDMCKA_03159;BGEAED_01754;BHJHEC_03183;BKLOHC_03263;BPEJMN_01356;BPLIPK_03510;CBPCJH_01772;CIMEKD_01454;DBCCLE_03070;DJMHJN_01766;DNOEHN_03358;DOFGLF_01162;DPLIOB_01473;EBKMEK_01662;EEGMED_03802;EEMIBL_02868;EOJHMN_02919;EPBFME_02204;FDDMPP_01777;FGOACM_02846;FLEJOH_02864;FNACPH_02402;FNLDAG_03386;FOMADB_03703;GAGFCG_02317;GKEIOM_01661 | dihydropteroate synthase | ||
| 40 | group_2808 | gene_presence_absence | PE_PGRS45-like (group_2808) | group_2808 | Rv2615c | low confidence | PE_PGRS45 | PE-PGRS family protein PE_PGRS45 | Rv2615c | PE_PGRS45 | PE-PGRS family protein PE_PGRS45 | low | 92.66 | 43.35 | Low-confidence GenBank rescue; treat as tentative and keep the Panaroo cluster ID. | identity=92.66; coverage=43.35 | 47 | 50 | 0.9400 | 41 | 50 | 0.8200 | Check manually | -8.35 | 3.10671 | 0.8514-11.34 | 0.851448 | 11.3356 | 1.23e-05 | 9.5455 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(2943600..2944985) | matched_representative_sequence=group_2808 | 12_refound_505_pseudo;AEDLOG_03206;AEMPHK_01845;AFKOAF_01648;ANMCAC_01912;APAKNA_01272;BDILPO_02203;BDMCKA_03591;BGEAED_00635;BHJHEC_03539;BPEJMN_01192;BPLIPK_03095;CBPCJH_01764;CIMEKD_01807;CKHCDK_01801;DBCCLE_03632;DJMHJN_01421;DNOEHN_02314;DOFGLF_01154;DPLIOB_01867;EBKMEK_02857;EEGMED_01305;EEMIBL_02545;EOJHMN_00068;EPBFME_01812;FDDMPP_01433;FGOACM_01434;FLEJOH_03699;FNACPH_02001;FNLDAG_03769 | PE-PGRS family protein PE_PGRS45 | ||
| 41 | group_331 | gene_presence_absence | group_331 | group_331 | Rv2680 | none confidence | group_331 | hypothetical protein | Rv2680 | hypothetical protein | none | 23.67 | 42.16 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=23.67; coverage=42.16 | 49 | 50 | 0.9800 | 31 | 50 | 0.6200 | cases (rpoB 763031 T C present) | 1.99 | 20.4286 | 3.659-114.1 | 3.65888 | 114.059 | 0.0106 | 9.3272 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2996105..2996737 | matched_representative_sequence=22_refound_874 | 17_refound_683_pseudo;18_refound_767_pseudo;22_refound_874;23_refound_892_pseudo;33_refound_998;43_refound_1370_pseudo;46_refound_1483;47_refound_1503_pseudo;56_refound_1612_pseudo;58_refound_1645_pseudo;5_refound_354_pseudo;62_refound_1722_pseudo;63_refound_1733_pseudo;64_refound_1752_pseudo;67_refound_1809_pseudo;69_refound_1837_pseudo;71_refound_1890_pseudo;74_refound_1922;81_refound_2032;82_refound_2062_pseudo;85_refound_2120;87_refound_2142_pseudo;88_refound_2161;8_refound_410_pseudo;9_refound_428_pseudo;AEDLOG_02535;AFNKCG_02308;BHJHEC_00320;BPLIPK_00031;CKHCDK_03171 | hypothetical protein | |||
| 42 | group_3058 | gene_presence_absence | PE_PGRS57 | group_3058 | Rv3514 | none confidence | PE_PGRS57 | PE-PGRS family protein PE_PGRS57 | Rv3514 | PE_PGRS57 | PE-PGRS family protein PE_PGRS57 | none | 61.86 | 36.26 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=61.86; coverage=36.26 | 45 | 50 | 0.9000 | 35 | 50 | 0.7000 | Check manually | -5.18 | 3.61204 | 1.242-10.5 | 1.24241 | 10.5012 | 3.64e-05 | 9.2917 | Panaroo/Bakta+GenBank | nucleotide_similarity | 3945794..3950263 | matched_representative_sequence=group_3058 | AEDLOG_02224;AEDLOG_03443;AEMPHK_02560;AEMPHK_04119;AFKOAF_01912;AFKOAF_01913;AFKOAF_04116;AFNKCG_04221;ANMCAC_02837;ANMCAC_04068;APAKNA_02849;APAKNA_02973;APAKNA_02974;BDILPO_01470;BDILPO_04078;BGEAED_02067;BGEAED_02923;BPEJMN_02358;BPEJMN_04094;BPLIPK_02431;BPLIPK_02432;CBPCJH_02559;CBPCJH_02560;CIMEKD_02453;CIMEKD_04125;CKHCDK_01120;CKHCDK_01121;CKHCDK_04193;DJMHJN_02963;DJMHJN_04082 | PE-PGRS family protein PE_PGRS57 | ||
| 43 | cut1 | gene_presence_absence | cut1 | cut1 | Rv1758 | high confidence | ;cut1 | hypothetical protein;Cutinase cut1;cutinase Cut1 | Rv1758 | cut1 | cutinase | high | 100.0 | 100.0 | High-confidence GenBank-supported annotation. | identity=100.0; coverage=100.0 | 11 | 50 | 0.2200 | 36 | 50 | 0.7200 | controls (rpoB 763031 T C absent) | -2.09 | 0.115658 | 0.04725-0.2831 | 0.0472464 | 0.283128 | 0.000781 | 9.2194 | Panaroo/Bakta+GenBank | qualifier_exact | 1989042..1989566 | AEDLOG_04065;AFKOAF_04091;APAKNA_04004;BDILPO_04023;BDMCKA_04008;BDMCKA_04104;BKLOHC_02718;BKLOHC_04172;BPLIPK_04021;BPLIPK_04104;CBPCJH_04047;CKHCDK_04013;CKHCDK_04180;DOFGLF_04006;DPLIOB_04001;EEGMED_03833;EEMIBL_04055;FLEJOH_03961;FNLDAG_03778;FOMADB_04097;GAGFCG_04061;GKEIOM_04112;HEJICF_04149;HFPBEP_03197;HIHJDO_02934;HLEDKO_04118;HLIGOK_04028;ICLPCH_03554;IJGDKF_04006;ILFCIO_03925 | cutinase | |||
| 44 | group_1513 | gene_presence_absence | PE13 | group_1513 | Rv1195 | none confidence | PE13 | hypothetical protein;PE domain-containing protein | Rv1195 | PE13 | PE family protein PE13 | none | 50.24 | 5.11 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=50.24; coverage=5.11 | 48 | 50 | 0.9600 | 25 | 50 | 0.5000 | cases (rpoB 763031 T C present) | 1.88 | 19.4 | 4.858-77.47 | 4.85817 | 77.4696 | 0.0228 | 8.9200 | Panaroo/Bakta+GenBank | nucleotide_similarity | 1339003..1339302 | matched_representative_sequence=group_1513 | AEMPHK_03384;AFNKCG_01903;ANMCAC_04045;APAKNA_03568;BDILPO_03249;BGEAED_02727;BHJHEC_04012;BPEJMN_04055;CIMEKD_03439;CKHCDK_04038;DBCCLE_02876;DJMHJN_04057;DNOEHN_04079;EBKMEK_04093;EEGMED_03020;EOJHMN_04063;EPBFME_04077;FDDMPP_03058;FGOACM_02701;FNACPH_04069;GAGFCG_04068;GKEIOM_04069;GKLDEJ_01188;GNKHBM_04095;HEJICF_04022;HIHJDO_03543;HLIGOK_04114;HNJHNP_04085;ICLPCH_03098;IDADDB_03997 | PE family protein PE13 | ||
| 45 | group_2236 | gene_presence_absence | esxO | group_2236 | Rv2346c | none confidence | esxO | ESAT-6 like protein EsxO | Rv2346c | esxO | ESAT-6 like protein EsxO | none | 40.20 | 4.89 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=40.20; coverage=4.89 | 2 | 50 | 0.0400 | 10 | 50 | 0.2000 | Check manually | 5.84 | 0.198822 | 0.04706-0.84 | 0.0470579 | 0.840032 | 0.000454 | 8.6734 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(2625888..2626172) | matched_representative_sequence=group_2236 | 0_refound_51_pseudo;13_refound_551_pseudo;3_refound_242_pseudo;95_refound_2330_pseudo;FNLDAG_02893;FOMADB_02364;HFPBEP_02402;JIEBBG_03035;NGOKMK_02598;NJPOJP_02349;NNCHJK_02455;OJHMIJ_02527 | ESAT-6 like protein EsxO | ||
| 46 | group_3418 | gene_presence_absence | group_3418 | group_3418 | Rv3103c | none confidence | group_3418 | hypothetical protein | Rv3103c | hypothetical protein | none | 34.12 | 2.58 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=34.12; coverage=2.58 | 3 | 50 | 0.0600 | 7 | 50 | 0.1400 | Check manually | 8.47 | 0.427368 | 0.1126-1.622 | 0.112601 | 1.62204 | 3.94e-05 | 8.6310 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(3471413..3471850) | matched_representative_sequence=group_3418 | BKLOHC_04183;FOMADB_04105;HFPBEP_04158;JEBLOM_04132;JIEBBG_04138;LPCJNG_04174;NJPOJP_04113;NNCHJK_04166;OHPLLA_08119;OJHMIJ_04130 | hypothetical protein | |||
| 47 | group_2734 | gene_presence_absence | Rv1004c (group_2734) | group_2734 | Rv1004c | high confidence | group_2734 | membrane protein | Rv1004c | membrane protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 49 | 50 | 0.9800 | 40 | 50 | 0.8000 | Check manually | -6.83 | 8.55556 | 1.471-49.75 | 1.47119 | 49.754 | 0.00399 | 8.4959 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(1120889..1122148) | matched_representative_sequence=2_refound_189 | 20_refound_851;2_refound_189;59_refound_1682_pseudo;70_refound_1882;AEDLOG_02820;AEMPHK_02865;AFKOAF_02553;AFNKCG_01412;ANMCAC_03186;APAKNA_02875;BDILPO_03118;BDMCKA_02315;BGEAED_00609;BHJHEC_02307;BPEJMN_02458;BPLIPK_01984;CBPCJH_02394;CIMEKD_02756;CKHCDK_01718;DBCCLE_02053;DJMHJN_00590;DNOEHN_02340;DOFGLF_02672;DPLIOB_02162;EBKMEK_02948;EEGMED_01438;EEMIBL_03287;EOJHMN_00042;EPBFME_02800;FDDMPP_00774 | membrane protein | |||
| 48 | group_1373 | gene_presence_absence | PE_PGRS17 | group_1373 | Rv0978c | none confidence | PE_PGRS17 | PE-PGRS family protein PE_PGRS17 | Rv0978c | PE_PGRS17 | PE-PGRS family protein PE_PGRS17 | none | 21.42 | 3.78 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=21.42; coverage=3.78 | 1 | 50 | 0.0200 | 10 | 50 | 0.2000 | Check manually | 6.83 | 0.116883 | 0.0201-0.6797 | 0.0200989 | 0.679722 | 0.00399 | 8.4959 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(1093361..1094356) | matched_representative_sequence=group_1373 | BKLOHC_03847;FOMADB_00411;HFPBEP_00114;JEBLOM_00109;KBDFIK_03875;LFDDMP_04139;LPCJNG_00736;NJPOJP_03813;NNCHJK_01558;ODNJBD_00716;OJHMIJ_01400 | PE-PGRS family protein PE_PGRS17 | ||
| 49 | group_2207 | gene_presence_absence | aroF | group_2207 | Rv2540c | high confidence | aroF | Chorismate synthase | Rv2540c | aroF | chorismate synthase | high | 100.00 | 96.87 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=96.87 | 49 | 50 | 0.9800 | 41 | 50 | 0.8200 | Check manually | -7.29 | 7.55422 | 1.286-44.38 | 1.28574 | 44.3838 | 0.00278 | 8.4732 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(2863207..2864412) | matched_representative_sequence=group_2207 | AEDLOG_02121;AEMPHK_01921;AFKOAF_02053;AFNKCG_01708;ANMCAC_01988;APAKNA_01194;BDILPO_02280;BDMCKA_03442;BGEAED_00712;BHJHEC_01970;BPEJMN_01116;BPLIPK_02157;CBPCJH_01687;CIMEKD_01731;CKHCDK_02647;DBCCLE_01508;DJMHJN_01497;DNOEHN_02260;DOFGLF_01077;DPLIOB_02761;EBKMEK_03497;EEGMED_02441;EEMIBL_02622;EOJHMN_00145;EPBFME_01736;FDDMPP_01510;FGOACM_02361;FLEJOH_02984;FNACPH_01925;FNLDAG_03431 | chorismate synthase | ||
| 50 | group_1760 | gene_presence_absence | Rv2159c (group_1760) | group_1760 | Rv2159c | high confidence | group_1760 | Alkyl hydroperoxide reductase Rv2159c | Rv2159c | hypothetical protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 49 | 50 | 0.9800 | 41 | 50 | 0.8200 | Check manually | -7.29 | 7.55422 | 1.286-44.38 | 1.28574 | 44.3838 | 0.00278 | 8.4732 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(2420631..2421665) | matched_representative_sequence=group_1760 | AEDLOG_03816;AEMPHK_00197;AFKOAF_01905;AFNKCG_02015;ANMCAC_03145;APAKNA_01016;BDILPO_02835;BDMCKA_03403;BGEAED_01313;BHJHEC_03379;BPEJMN_03572;BPLIPK_03697;CBPCJH_01542;CIMEKD_00252;CKHCDK_02923;DBCCLE_04025;DJMHJN_02545;DNOEHN_03573;DOFGLF_02293;DPLIOB_03224;EBKMEK_02115;EEGMED_00812;EEMIBL_00178;EOJHMN_02165;EPBFME_00058;FDDMPP_02795;FGOACM_03072;FLEJOH_03788;FNACPH_03240;FNLDAG_02165 | hypothetical protein | |||
| 51 | menF | gene_presence_absence | Rv1005c (menF) | menF | Rv1005c | high confidence | menF | Isochorismate synthase MenF | Rv1005c | para-aminobenzoate synthase component I | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 49 | 50 | 0.9800 | 41 | 50 | 0.8200 | Check manually | -7.29 | 7.55422 | 1.286-44.38 | 1.28574 | 44.3838 | 0.00278 | 8.4732 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(1122222..1123598) | matched_representative_sequence=menF | AEDLOG_02819;AEMPHK_02866;AFKOAF_02552;AFNKCG_01411;ANMCAC_03187;APAKNA_02876;BDILPO_03117;BDMCKA_02316;BGEAED_00608;BHJHEC_02308;BPEJMN_02459;BPLIPK_01983;CBPCJH_02395;CIMEKD_02757;CKHCDK_01717;DBCCLE_02054;DJMHJN_00591;DNOEHN_02341;DOFGLF_02671;DPLIOB_02163;EBKMEK_02949;EEGMED_01437;EEMIBL_03288;EOJHMN_00041;EPBFME_02801;FDDMPP_00773;FGOACM_01971;FLEJOH_01957;FNACPH_02537;FNLDAG_04024 | para-aminobenzoate synthase component I | |||
| 52 | group_777 | gene_presence_absence | murG-like (group_777) | group_777 | Rv2153c | low confidence | murG | hypothetical protein;UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase | Rv2153c | murG | UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol-N-acetylglucosaminetransferase | low | 100.00 | 44.24 | Low-confidence GenBank rescue; treat as tentative and keep the Panaroo cluster ID. | identity=100.00; coverage=44.24 | 49 | 50 | 0.9800 | 41 | 50 | 0.8200 | Check manually | -7.29 | 7.55422 | 1.286-44.38 | 1.28574 | 44.3838 | 0.00278 | 8.4732 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(2412119..2413351) | matched_representative_sequence=group_777 | AEDLOG_03810;AEMPHK_00203;AFKOAF_01899;AFNKCG_02009;ANMCAC_03139;APAKNA_01022;BDILPO_02829;BDMCKA_03409;BGEAED_01307;BHJHEC_03373;BPEJMN_03566;BPLIPK_03703;CBPCJH_01548;CIMEKD_00246;CKHCDK_02917;DBCCLE_03389;DJMHJN_02551;DNOEHN_03579;DOFGLF_02299;DPLIOB_03218;EBKMEK_02109;EEGMED_00806;EEMIBL_00184;EOJHMN_02159;EPBFME_00052;FDDMPP_02801;FGOACM_03078;FLEJOH_03782;FNACPH_03234;FNLDAG_03110 | UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol-N-acetylglucosaminetransferase | ||
| 53 | group_504 | gene_presence_absence | PPE30 | group_504 | Rv1802 | high confidence | PPE30 | Uncharacterized PPE family protein PPE30 | Rv1802 | PPE30 | PPE family protein PPE30 | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 49 | 50 | 0.9800 | 41 | 50 | 0.8200 | Check manually | -7.29 | 7.55422 | 1.286-44.38 | 1.28574 | 44.3838 | 0.00278 | 8.4732 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 2043384..2044775 | matched_representative_sequence=group_504 | AEDLOG_03907;AEMPHK_01469;AFKOAF_01371;AFNKCG_03952;ANMCAC_01496;APAKNA_00974;BDILPO_01796;BDMCKA_02641;BGEAED_02403;BHJHEC_02897;BPEJMN_03724;BPLIPK_02947;CBPCJH_01400;CIMEKD_01186;CKHCDK_04079;DBCCLE_03580;DJMHJN_01248;DNOEHN_02645;DOFGLF_03491;DPLIOB_04096;EBKMEK_03841;EEGMED_03359;EEMIBL_02020;EOJHMN_03295;EPBFME_01267;FDDMPP_00960;FGOACM_03500;FLEJOH_04033;FNACPH_01559;FNLDAG_04056 | PPE family protein PPE30 | ||
| 54 | group_563 | gene_presence_absence | group_563 | group_563 | Rv0025 | none confidence | group_563 | hypothetical protein | Rv0025 | hypothetical protein | none | 35.03 | 1.53 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=35.03; coverage=1.53 | 1 | 50 | 0.0200 | 9 | 50 | 0.1800 | Check manually | 7.29 | 0.132376 | 0.02253-0.7778 | 0.0225307 | 0.77776 | 0.00278 | 8.4732 | Panaroo/Bakta+GenBank | nucleotide_similarity | 29245..29607 | matched_representative_sequence=12_refound_477 | 12_refound_477;41_refound_1318;BKLOHC_02581;JEBLOM_04174;KBDFIK_03935;LFDDMP_04168;LPCJNG_04203;NNCHJK_04079;ODNJBD_04195;OJHMIJ_04035 | hypothetical protein | |||
| 55 | group_3020 | gene_presence_absence | PE_PGRS29 | group_3020 | Rv1468c | high confidence | PE_PGRS29 | hypothetical protein;PE family protein | Rv1468c | PE_PGRS29 | PE-PGRS family protein PE_PGRS29 | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 48 | 50 | 0.9600 | 45 | 50 | 0.9000 | Check manually | -15.3 | 2.34505 | 0.4983-11.04 | 0.498336 | 11.0353 | 5.78e-05 | 8.4677 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(1655609..1656721) | matched_representative_sequence=2_refound_193 | 12_refound_511;2_refound_193;36_refound_1055_pseudo;37_refound_1067_pseudo;41_refound_1358;83_refound_2107_pseudo;94_refound_2294_pseudo;95_refound_2407;AEDLOG_01061;AEMPHK_03873;AFKOAF_00109;AFNKCG_01011;ANMCAC_03919;APAKNA_02694;BDILPO_01564;BDMCKA_03722;BGEAED_01372;BHJHEC_03721;BPEJMN_03931;BPLIPK_03882;CBPCJH_01430;CIMEKD_03884;CKHCDK_03599;DJMHJN_04003;DNOEHN_03810;DOFGLF_00822;DPLIOB_00745;EBKMEK_03803;EEGMED_00011;EEMIBL_03129 | PE-PGRS family protein PE_PGRS29 | ||
| 56 | group_3135 | gene_presence_absence | PE_PGRS22 | group_3135 | Rv1091 | none confidence | PE_PGRS22 | hypothetical protein;PE family protein | Rv1091 | PE_PGRS22 | PE-PGRS family protein PE_PGRS22 | none | 99.80 | 37.90 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=99.80; coverage=37.90 | 47 | 50 | 0.9400 | 36 | 50 | 0.7200 | Check manually | -4.67 | 5.39139 | 1.553-18.71 | 1.55325 | 18.7137 | 0.000999 | 8.4311 | Panaroo/Bakta+GenBank | nucleotide_similarity | 1216469..1219030 | matched_representative_sequence=group_3135 | AEDLOG_03118;AEDLOG_04088;AEMPHK_03306;AEMPHK_03742;AFKOAF_03638;AFNKCG_01483;ANMCAC_03551;ANMCAC_03839;APAKNA_03433;APAKNA_03870;BDILPO_02373;BDMCKA_02679;BGEAED_03198;BGEAED_04089;BHJHEC_02758;BPEJMN_02286;BPLIPK_03181;BPLIPK_04087;CBPCJH_03171;CBPCJH_04061;CIMEKD_03234;CIMEKD_03773;CIMEKD_03774;CKHCDK_00884;CKHCDK_04217;DBCCLE_02450;DJMHJN_02276;DNOEHN_03093;DNOEHN_04048;DOFGLF_01304 | PE-PGRS family protein PE_PGRS22 | ||
| 57 | group_2937 | gene_presence_absence | cobG-like (group_2937) | group_2937 | Rv2064 | low confidence | cobG | hypothetical protein;Precorrin-3B synthase | Rv2064 | cobG | precorrin-3B synthase | low | 99.91 | 51.92 | Low-confidence GenBank rescue; treat as tentative and keep the Panaroo cluster ID. | identity=99.91; coverage=51.92 | 49 | 50 | 0.9800 | 42 | 50 | 0.8400 | Check manually | -7.8 | 6.6 | 1.109-39.28 | 1.10908 | 39.2759 | 0.00212 | 8.3961 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2321451..2322542 | matched_representative_sequence=group_2937 | 82_refound_2095_pseudo;AEDLOG_03683;AEMPHK_03401;AFKOAF_02781;AFNKCG_01961;ANMCAC_03486;APAKNA_01112;BDILPO_03570;BDMCKA_02928;BGEAED_01216;BHJHEC_03428;BPEJMN_03223;BPLIPK_02448;CBPCJH_01641;CIMEKD_03420;CKHCDK_03068;DBCCLE_02737;DJMHJN_03872;DNOEHN_02778;DOFGLF_03119;DPLIOB_03335;EBKMEK_02017;EEGMED_02891;EEMIBL_00274;EOJHMN_02988;EPBFME_03291;FDDMPP_03806;FGOACM_02937;FLEJOH_03353;FNACPH_03499 | precorrin-3B synthase | ||
| 58 | group_3244 | gene_presence_absence | Rv1356c (group_3244) | group_3244 | Rv1356c | high confidence | group_3244 | Uncharacterized protein Rv1356c | Rv1356c | hypothetical protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(1524029..1524820) | matched_representative_sequence=group_3244 | AEDLOG_02264;AEMPHK_03221;AFKOAF_03591;AFNKCG_01532;ANMCAC_02979;BDILPO_01511;BDMCKA_02112;BGEAED_02802;BHJHEC_02108;BKLOHC_01438;BPEJMN_02618;BPLIPK_02391;CBPCJH_02134;CIMEKD_03100;CKHCDK_01161;DBCCLE_01818;DJMHJN_03150;DNOEHN_03070;DOFGLF_02957;DPLIOB_01608;EBKMEK_02656;EEGMED_01095;EOJHMN_02435;EPBFME_02858;FDDMPP_01283;FGOACM_02753;FLEJOH_01182;FNACPH_03043;FNLDAG_01624;FOMADB_02486 | hypothetical protein | |||
| 59 | group_2719 | gene_presence_absence | moeY | group_2719 | Rv1355c | high confidence | moeY | hypothetical protein;Rv1355c family protein;THIF-type NAD/FAD binding fold domain-containing protein | Rv1355c | moeY | molybdopterin biosynthesis protein MoeY | high | 99.95 | 92.74 | High-confidence GenBank-supported annotation. | identity=99.95; coverage=92.74 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(1521885..1524032) | matched_representative_sequence=group_2719 | AEDLOG_02265;AEMPHK_03220;AFKOAF_03590;AFNKCG_01533;ANMCAC_02978;BDILPO_01512;BDMCKA_02110;BDMCKA_02111;BGEAED_02801;BHJHEC_02107;BKLOHC_01437;BPEJMN_02617;BPLIPK_02390;CBPCJH_02135;CIMEKD_03101;CKHCDK_01162;DBCCLE_01817;DJMHJN_03151;DNOEHN_03069;DOFGLF_02958;DPLIOB_01607;EBKMEK_02657;EEGMED_01096;EOJHMN_02434;EPBFME_02859;FDDMPP_01282;FGOACM_02752;FGOACM_03110;FLEJOH_01183;FNACPH_03044 | molybdopterin biosynthesis protein MoeY | ||
| 60 | group_2341 | gene_presence_absence | lprP | group_2341 | Rv0962c | none confidence | lprP | Uncharacterized protein Rv2277c | Rv0962c | lprP | lipoprotein LprP | none | 40.25 | 1.75 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=40.25; coverage=1.75 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(1074440..1075114) | matched_representative_sequence=group_2341 | AEDLOG_02584;AEMPHK_00077;AFKOAF_03272;AFNKCG_00619;ANMCAC_00965;BDILPO_00550;BDMCKA_01523;BGEAED_01890;BHJHEC_00917;BKLOHC_00999;BPEJMN_00539;BPLIPK_01467;CBPCJH_03700;CIMEKD_00372;CKHCDK_01019;DBCCLE_00440;DJMHJN_02127;DNOEHN_00117;DOFGLF_03743;DPLIOB_01717;EBKMEK_00518;EEGMED_00370;EOJHMN_00937;EPBFME_00178;FDDMPP_02617;FGOACM_02578;FLEJOH_01416;FNACPH_00851;FNLDAG_00252;FOMADB_01054 | lipoprotein LprP | ||
| 61 | cyp121 | gene_presence_absence | cyp121 | cyp121 | Rv2276 | high confidence | ;cyp121 | hypothetical protein;Mycocyclosin synthase;mycocyclosin synthase Cyp121 | Rv2276 | cyp121 | cytochrome P450 Cyp121 | high | 100.0 | 100.0 | High-confidence GenBank-supported annotation. | identity=100.0; coverage=100.0 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | qualifier_exact | 2547749..2548939 | AEDLOG_02583;AEMPHK_00078;AFKOAF_03271;AFNKCG_00618;ANMCAC_00964;BDILPO_00549;BDMCKA_01524;BGEAED_01889;BHJHEC_00918;BKLOHC_01000;BPEJMN_00540;BPLIPK_01466;CBPCJH_03701;CIMEKD_00371;CKHCDK_01020;DBCCLE_00439;DJMHJN_02128;DNOEHN_00116;DOFGLF_03744;DPLIOB_01718;EBKMEK_00517;EEGMED_00369;EOJHMN_00938;EPBFME_00177;FDDMPP_02616;FGOACM_02579;FLEJOH_01417;FNACPH_00850;FNLDAG_00253;FOMADB_01053 | cytochrome P450 Cyp121 | |||
| 62 | group_2198 | gene_presence_absence | Rv2273-like (group_2198) | group_2198 | Rv2273 | medium confidence | group_2198 | Uncharacterized protein Rv2273 | Rv2273 | transmembrane protein | medium | 99.70 | 77.88 | Medium-confidence locus-level GenBank rescue. | identity=99.70; coverage=77.88 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2546102..2546431 | matched_representative_sequence=group_2198 | AEDLOG_02581;AEMPHK_00080;AFKOAF_03269;AFNKCG_00616;ANMCAC_00962;BDILPO_00547;BDMCKA_01526;BGEAED_01887;BHJHEC_00920;BKLOHC_01002;BPEJMN_00542;BPLIPK_01464;CBPCJH_03703;CIMEKD_00369;CKHCDK_01022;DBCCLE_00437;DJMHJN_02130;DNOEHN_00114;DOFGLF_03746;DPLIOB_01720;EBKMEK_00515;EEGMED_00367;EOJHMN_00940;EPBFME_00175;FDDMPP_02614;FGOACM_02581;FLEJOH_01419;FNACPH_00848;FNLDAG_00255;FOMADB_01051 | transmembrane protein | |||
| 63 | group_1858 | gene_presence_absence | Rv2272 (group_1858) | group_1858 | Rv2272 | high confidence | group_1858 | DUF202 domain-containing protein | Rv2272 | transmembrane protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 2545737..2546105 | matched_representative_sequence=group_1858 | AEDLOG_02580;AEMPHK_00081;AFKOAF_03268;AFNKCG_00615;ANMCAC_00961;BDILPO_00546;BDMCKA_01527;BGEAED_01886;BHJHEC_00921;BKLOHC_01003;BPEJMN_00543;BPLIPK_01463;CBPCJH_03704;CIMEKD_00368;CKHCDK_01023;DBCCLE_00436;DJMHJN_02131;DNOEHN_00113;DOFGLF_03747;DPLIOB_01721;EBKMEK_00514;EEGMED_00366;EOJHMN_00941;EPBFME_00174;FDDMPP_02613;FGOACM_02582;FLEJOH_01420;FNACPH_00847;FNLDAG_00256;FOMADB_01050 | transmembrane protein | |||
| 64 | group_1609 | gene_presence_absence | Rv2102 (group_1609) | group_1609 | Rv2102 | high confidence | group_1609 | hypothetical protein;Uncharacterized protein Rv2102 | Rv2102 | hypothetical protein | high | 100.00 | 85.97 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=85.97 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 2363391..2364107 | matched_representative_sequence=group_1609 | 95_refound_2370_pseudo;AEDLOG_03420;AEMPHK_03920;AFKOAF_03203;AFNKCG_03053;ANMCAC_03449;BDILPO_02775;BDMCKA_03932;BGEAED_01253;BHJHEC_03904;BKLOHC_00248;BPEJMN_03950;BPLIPK_02486;CBPCJH_01603;CIMEKD_03903;CKHCDK_03959;DBCCLE_03990;DJMHJN_02606;DNOEHN_02741;DOFGLF_02354;DPLIOB_04054;EBKMEK_02054;EEGMED_00751;EOJHMN_03798;EPBFME_03328;FDDMPP_02856;FGOACM_03282;FLEJOH_03504;FNACPH_03532;FNLDAG_03926 | hypothetical protein | |||
| 65 | group_1521 | gene_presence_absence | Rv2271 (group_1521) | group_1521 | Rv2271 | high confidence | group_1521 | hypothetical protein | Rv2271 | hypothetical protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 2545332..2545631 | matched_representative_sequence=group_1521 | AEDLOG_02579;AEMPHK_00082;AFKOAF_03267;AFNKCG_00614;ANMCAC_00960;BDILPO_00545;BDMCKA_01528;BGEAED_01885;BHJHEC_00922;BKLOHC_01004;BPEJMN_00544;BPLIPK_01462;CBPCJH_03705;CIMEKD_00367;CKHCDK_01024;DBCCLE_00435;DJMHJN_02132;DNOEHN_00112;DOFGLF_03748;DPLIOB_01722;EBKMEK_00513;EEGMED_00365;EOJHMN_00942;EPBFME_00173;FDDMPP_02612;FGOACM_02583;FLEJOH_01421;FNACPH_00846;FNLDAG_00257;FOMADB_01049 | hypothetical protein | |||
| 66 | group_962 | gene_presence_absence | Rv2275 (group_962) | group_962 | Rv2275 | high confidence | group_962 | hypothetical protein;Cyclo(L-tyrosyl-L-tyrosyl) synthase | Rv2275 | cyclo(L-tyrosyl-L-tyrosyl) synthase | high | 99.89 | 89.77 | High-confidence locus-level GenBank rescue. | identity=99.89; coverage=89.77 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2546883..2547752 | matched_representative_sequence=group_962 | AEDLOG_02582;AEMPHK_00079;AFKOAF_03270;AFNKCG_00617;ANMCAC_00963;BDILPO_00548;BDMCKA_01525;BGEAED_01888;BHJHEC_00919;BKLOHC_01001;BPEJMN_00541;BPLIPK_01465;CBPCJH_03702;CIMEKD_00370;CKHCDK_01021;DBCCLE_00438;DJMHJN_02129;DNOEHN_00115;DOFGLF_03745;DPLIOB_01719;EBKMEK_00516;EEGMED_00368;EOJHMN_00939;EPBFME_00176;FDDMPP_02615;FGOACM_02580;FLEJOH_01418;FNACPH_00849;FNLDAG_00254;FOMADB_01052 | cyclo(L-tyrosyl-L-tyrosyl) synthase | |||
| 67 | group_252 | gene_presence_absence | Rv0106 (group_252) | group_252 | Rv0106 | high confidence | group_252 | Diguanylate phosphodiesterase | Rv0106 | hypothetical protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 50 | 50 | 1.0000 | 45 | 50 | 0.9000 | cases (rpoB 763031 T C present) | 2.82 | 12.2088 | 0.6567-227 | 0.65669 | 226.979 | 0.0166 | 8.3897 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 124374..125570 | matched_representative_sequence=group_2526 | AEDLOG_02266;AEMPHK_03219;AFKOAF_03589;AFNKCG_01534;ANMCAC_02977;BDILPO_01513;BDMCKA_02109;BGEAED_02800;BHJHEC_02106;BKLOHC_01436;BPEJMN_02616;BPLIPK_02389;CBPCJH_02136;CIMEKD_03102;CKHCDK_01163;DBCCLE_01816;DJMHJN_03152;DNOEHN_03068;DOFGLF_02959;DPLIOB_01606;EBKMEK_02658;EEGMED_01097;EOJHMN_02433;EPBFME_02860;FDDMPP_01281;FGOACM_03111;FLEJOH_01184;FNACPH_03045;FNLDAG_01622;FOMADB_02483 | hypothetical protein | |||
| 68 | group_324 | gene_presence_absence | Rv1356c (group_324) | group_324 | Rv1356c | high confidence | group_324 | hypothetical protein | Rv1356c | hypothetical protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 0 | 50 | 0.0000 | 6 | 50 | 0.1200 | controls (rpoB 763031 T C absent) | -2.49 | 0.0677837 | 0.003713-1.238 | 0.00371262 | 1.23757 | 0.0317 | 8.3819 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(1524029..1524820) | matched_representative_sequence=group_3244 | BGEAED_03305;BPLIPK_03331;FLEJOH_04157;GKEIOM_02891;IPDLAB_03394;NOBKKO_03681 | hypothetical protein | |||
| 69 | group_3081 | gene_presence_absence | PE_PGRS26 | group_3081 | Rv1441c | none confidence | PE_PGRS26 | hypothetical protein;PE family protein | Rv1441c | PE_PGRS26 | PE-PGRS family protein PE_PGRS26 | none | 51.13 | 28.05 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=51.13; coverage=28.05 | 43 | 50 | 0.8600 | 36 | 50 | 0.7200 | Check manually | -4.32 | 2.30411 | 0.8602-6.172 | 0.860232 | 6.1715 | 7.24e-05 | 8.3445 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(1618209..1619684) | matched_representative_sequence=group_3081 | AEDLOG_03489;AEDLOG_04050;AEMPHK_02514;AFKOAF_01959;AFKOAF_03763;AFNKCG_01177;ANMCAC_02791;APAKNA_02927;BDILPO_01424;BGEAED_02969;BGEAED_02970;BPEJMN_02404;BPLIPK_03456;BPLIPK_03996;CBPCJH_02512;CBPCJH_02513;CIMEKD_02499;CKHCDK_02021;DJMHJN_02917;DNOEHN_03244;DOFGLF_01485;DPLIOB_02523;EBKMEK_02569;EBKMEK_04019;EEGMED_02319;EEMIBL_02190;EEMIBL_02191;EOJHMN_02805;EPBFME_02685;FDDMPP_01369 | PE-PGRS family protein PE_PGRS26 | ||
| 70 | group_2884 | gene_presence_absence | Rv1066-like (group_2884) | group_2884 | Rv1066 | medium confidence | group_2884 | Rhodanese domain-containing protein;hypothetical protein | Rv1066 | hypothetical protein | medium | 91.43 | 82.43 | Medium-confidence locus-level GenBank rescue. | identity=91.43; coverage=82.43 | 49 | 50 | 0.9800 | 42 | 50 | 0.8400 | Check manually | -7.44 | 6.6 | 1.109-39.28 | 1.10908 | 39.2759 | 0.00255 | 8.3159 | Panaroo/Bakta+GenBank | nucleotide_similarity | 1187998..1188393 | matched_representative_sequence=group_2884 | AEDLOG_03931;AEMPHK_03851;AFKOAF_03441;AFNKCG_02881;ANMCAC_03941;APAKNA_03948;BDILPO_02400;BDMCKA_03744;BGEAED_03954;BHJHEC_03739;BPEJMN_02312;BPLIPK_03904;CBPCJH_03933;CIMEKD_03882;CKHCDK_03464;DBCCLE_03758;DJMHJN_02249;DNOEHN_03832;DOFGLF_01277;DPLIOB_03623;EBKMEK_03897;EEGMED_03416;EEMIBL_03994;EOJHMN_03773;EPBFME_03963;FDDMPP_02070;FGOACM_03592;FLEJOH_03394;FNACPH_03604;FNLDAG_03022 | hypothetical protein | |||
| 71 | group_2414 | gene_presence_absence | Rv0613c (group_2414) | group_2414 | Rv0613c | high confidence | group_2414 | hypothetical protein;Zinc-binding protein | Rv0613c | hypothetical protein | high | 99.96 | 84.93 | High-confidence locus-level GenBank rescue. | identity=99.96; coverage=84.93 | 49 | 50 | 0.9800 | 42 | 50 | 0.8400 | Check manually | -7.44 | 6.6 | 1.109-39.28 | 1.10908 | 39.2759 | 0.00255 | 8.3159 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(706948..709515) | matched_representative_sequence=group_2414 | 94_refound_2284_pseudo;AEDLOG_00612;AEMPHK_00292;AFKOAF_02664;AFNKCG_02540;ANMCAC_00194;APAKNA_03696;BDILPO_01951;BDMCKA_00652;BGEAED_01493;BHJHEC_01321;BPEJMN_00348;BPLIPK_00893;CBPCJH_01225;CIMEKD_01339;CKHCDK_00134;DBCCLE_01987;DJMHJN_00765;DNOEHN_00870;DOFGLF_00292;DPLIOB_02809;EBKMEK_00968;EEGMED_02084;EEMIBL_00395;EOJHMN_02093;EPBFME_00595;FDDMPP_00359;FGOACM_00393;FLEJOH_02628;FNACPH_00356 | hypothetical protein | |||
| 72 | group_3388 | gene_presence_absence | tatD | group_3388 | Rv1008 | none confidence | tatD | deoxyribonuclease TatD | Rv1008 | tatD | deoxyribonuclease TatD | none | 33.13 | 7.25 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=33.13; coverage=7.25 | 1 | 50 | 0.0200 | 8 | 50 | 0.1600 | Check manually | 7.29 | 0.151515 | 0.02546-0.9017 | 0.0254609 | 0.90165 | 0.00278 | 8.2784 | Panaroo/Bakta+GenBank | nucleotide_similarity | 1127089..1127883 | matched_representative_sequence=group_3388 | BKLOHC_04150;HFPBEP_04000;JEBLOM_04070;LFDDMP_04024;LPCJNG_04080;NJPOJP_03916;NNCHJK_03702;ODNJBD_04116;OJHMIJ_03954 | deoxyribonuclease TatD | ||
| 73 | group_3383 | gene_presence_absence | group_3383 | group_3383 | Rv1638A | none confidence | group_3383 | hypothetical protein | Rv1638A | hypothetical protein | none | 28.19 | 3.55 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=28.19; coverage=3.55 | 1 | 50 | 0.0200 | 8 | 50 | 0.1600 | Check manually | 7.29 | 0.151515 | 0.02546-0.9017 | 0.0254609 | 0.90165 | 0.00279 | 8.2769 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(1846716..1846973) | matched_representative_sequence=80_refound_1995 | 80_refound_1995;HFPBEP_04047;JEBLOM_03807;KBDFIK_03521;LFDDMP_03914;LPCJNG_03852;NJPOJP_04018;ODNJBD_04033;OJHMIJ_04030 | hypothetical protein | |||
| 74 | group_2903 | gene_presence_absence | PE_PGRS34 | group_2903 | Rv1840c | high confidence | PE_PGRS34 | hypothetical protein;PE family protein;Uncharacterized PE-PGRS family protein PE_PGRS34 | Rv1840c | PE_PGRS34 | PE-PGRS family protein PE_PGRS34 | high | 99.90 | 82.66 | High-confidence GenBank-supported annotation. | identity=99.90; coverage=82.66 | 48 | 50 | 0.9600 | 40 | 50 | 0.8000 | Check manually | -5.77 | 5.02963 | 1.19-21.25 | 1.19043 | 21.2504 | 0.00119 | 8.2549 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(2087971..2089518) | matched_representative_sequence=group_2903 | 82_refound_2094_pseudo;AEDLOG_01865;AEMPHK_01432;AFKOAF_01408;ANMCAC_01460;APAKNA_00938;BDILPO_01759;BDMCKA_03523;BGEAED_02366;BHJHEC_03493;BPEJMN_01699;BPLIPK_01592;CBPCJH_01363;CIMEKD_01149;CKHCDK_00387;DBCCLE_03449;DJMHJN_01285;DNOEHN_01813;DOFGLF_01389;DPLIOB_00283;EBKMEK_02202;EEGMED_02721;EEMIBL_01984;EOJHMN_01073;EPBFME_01304;FDDMPP_00997;FGOACM_01391;FLEJOH_01559;FNACPH_01522;FOMADB_03124 | PE-PGRS family protein PE_PGRS34 | ||
| 75 | group_2987 | gene_presence_absence | Rv2652c (group_2987) | group_2987 | Rv2652c | high confidence | group_2987 | hypothetical protein;phage terminase small subunit P27 family | Rv2652c | prophage protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 44 | 50 | 0.8800 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -4.23 | 0.0677837 | 0.003713-1.238 | 0.00371262 | 1.23757 | 0.0433 | 8.2464 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(2975928..2976554) | matched_representative_sequence=group_2987 | AEDLOG_03247;AEMPHK_03543;AFKOAF_02618;AFNKCG_03089;ANMCAC_01872;APAKNA_01312;BDILPO_03725;BDMCKA_03656;BGEAED_03816;BHJHEC_03620;BKLOHC_03953;BPEJMN_01232;BPLIPK_03055;CBPCJH_03598;CIMEKD_03568;CKHCDK_03586;DBCCLE_03654;DJMHJN_01381;DNOEHN_03530;DOFGLF_03371;DPLIOB_03677;EBKMEK_03863;EEGMED_03375;EEMIBL_03921;EOJHMN_03171;EPBFME_01847;FDDMPP_01393;FGOACM_03546;FLEJOH_03657;FNACPH_02041 | prophage protein | |||
| 76 | group_360 | gene_presence_absence | Rv2651c (group_360) | group_360 | Rv2651c | high confidence | group_360 | PhiRv2 prophage protease;Prohead serine protease domain-containing protein | Rv2651c | prophage protease | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 44 | 50 | 0.8800 | 50 | 50 | 1.0000 | controls (rpoB 763031 T C absent) | -4.23 | 0.0677837 | 0.003713-1.238 | 0.00371262 | 1.23757 | 0.0433 | 8.2464 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(2975242..2975775) | matched_representative_sequence=group_360 | AEDLOG_03246;AEMPHK_03542;AFKOAF_02617;AFNKCG_03090;ANMCAC_01873;APAKNA_01311;BDILPO_03726;BDMCKA_03655;BGEAED_03815;BHJHEC_03621;BKLOHC_03952;BPEJMN_01231;BPLIPK_03056;CBPCJH_03599;CIMEKD_03569;CKHCDK_03585;DBCCLE_03653;DJMHJN_01382;DNOEHN_03531;DOFGLF_03370;DPLIOB_03678;EBKMEK_03862;EEGMED_03376;EEMIBL_03920;EOJHMN_03172;EPBFME_01846;FDDMPP_01394;FGOACM_03547;FLEJOH_03658;FNACPH_02040 | prophage protease | |||
| 77 | group_3208 | gene_presence_absence | group_3208 | group_3208 | Rv0008c | none confidence | group_3208 | cell wall synthesis protein CwsA | Rv0008c | cell wall synthesis protein CwsA | none | 42.28 | 5.65 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=42.28; coverage=5.65 | 1 | 50 | 0.0200 | 7 | 50 | 0.1400 | Check manually | 8.18 | 0.175758 | 0.02906-1.063 | 0.029059 | 1.06304 | 0.00187 | 8.2365 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(11874..12311) | matched_representative_sequence=40_refound_1157 | 40_refound_1157;BKLOHC_03499;JEBLOM_03201;LFDDMP_02846;LPCJNG_03244;NJPOJP_03848;NNCHJK_03926;ODNJBD_03303 | cell wall synthesis protein CwsA | |||
| 78 | group_1834 | gene_presence_absence | PE18 | group_1834 | Rv1788 | none confidence | PE18 | PE family protein PE18 | Rv1788 | PE18 | PE family protein PE18 | none | 21.10 | 4.24 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=21.10; coverage=4.24 | 1 | 50 | 0.0200 | 7 | 50 | 0.1400 | Check manually | 8.18 | 0.175758 | 0.02906-1.063 | 0.029059 | 1.06304 | 0.00187 | 8.2365 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2026477..2026776 | matched_representative_sequence=group_1834 | BKLOHC_03500;JEBLOM_03202;KBDFIK_03991;LFDDMP_02845;LPCJNG_03245;NJPOJP_03849;NNCHJK_03925;ODNJBD_03302 | PE family protein PE18 | ||
| 79 | group_1734 | gene_presence_absence | group_1734 | group_1734 | Rv0108c | none confidence | group_1734 | Transposase IS701-like DDE domain-containing protein | Rv0108c | hypothetical protein | none | 46.71 | 6.49 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=46.71; coverage=6.49 | 11 | 50 | 0.2200 | 3 | 50 | 0.0600 | cases (rpoB 763031 T C present) | 3.11 | 3.95118 | 1.111-14.05 | 1.11098 | 14.0523 | 0.000606 | 8.1998 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(130895..131104) | matched_representative_sequence=group_1734 | AFNKCG_01943;CKHCDK_04194;FDDMPP_03822;HEJICF_02889;IJKJHL_03163;JGDOPI_02947;KBDFIK_02198;MHDACH_04162;MLLPLE_04088;NBJBMA_04125;NMJEMD_04096;OJOIGL_04141;OLKJCH_02957;ONNOIP_03965 | hypothetical protein | |||
| 80 | group_3375 | gene_presence_absence | group_3375 | group_3375 | Rv3069 | none confidence | group_3375 | fluoride ion transporter CrcB | Rv3069 | fluoride ion transporter CrcB | none | 39.15 | 4.90 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=39.15; coverage=4.90 | 1 | 50 | 0.0200 | 7 | 50 | 0.1400 | Check manually | 7.8 | 0.175758 | 0.02906-1.063 | 0.029059 | 1.06304 | 0.00212 | 8.1820 | Panaroo/Bakta+GenBank | nucleotide_similarity | 3433692..3434090 | matched_representative_sequence=group_3375 | JEBLOM_04030;KBDFIK_03577;LFDDMP_03834;LPCJNG_03999;NJPOJP_04039;NNCHJK_04095;ODNJBD_03975;OJHMIJ_04058 | fluoride ion transporter CrcB | |||
| 81 | group_1581 | gene_presence_absence | group_1581 | group_1581 | Rv0025 | none confidence | group_1581 | hypothetical protein | Rv0025 | hypothetical protein | none | 32.96 | 2.31 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=32.96; coverage=2.31 | 1 | 50 | 0.0200 | 7 | 50 | 0.1400 | Check manually | 7.36 | 0.175758 | 0.02906-1.063 | 0.029059 | 1.06304 | 0.00269 | 8.0786 | Panaroo/Bakta+GenBank | nucleotide_similarity | 29245..29607 | matched_representative_sequence=group_1581 | BKLOHC_03595;HFPBEP_03929;JEBLOM_03250;LFDDMP_03019;LPCJNG_03351;NNCHJK_03972;ODNJBD_03369;OJHMIJ_03903 | hypothetical protein | |||
| 82 | group_1005 | gene_presence_absence | bcpB | group_1005 | Rv1608c | none confidence | bcpB | peroxiredoxin | Rv1608c | bcpB | peroxiredoxin | none | 31.59 | 1.86 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=31.59; coverage=1.86 | 1 | 50 | 0.0200 | 7 | 50 | 0.1400 | Check manually | 7.36 | 0.175758 | 0.02906-1.063 | 0.029059 | 1.06304 | 0.00269 | 8.0786 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(1807298..1807762) | matched_representative_sequence=group_1005 | 13_refound_571_pseudo;3_refound_259_pseudo;95_refound_2355_pseudo;BKLOHC_03856;HFPBEP_02913;LFDDMP_03601;NNCHJK_02980;OJHMIJ_02933 | peroxiredoxin | ||
| 83 | group_335 | gene_presence_absence | Rv3054c (group_335) | group_335 | Rv3054c | high confidence | group_335 | hypothetical protein | Rv3054c | hypothetical protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 1 | 50 | 0.0200 | 7 | 50 | 0.1400 | Check manually | 7.36 | 0.175758 | 0.02906-1.063 | 0.029059 | 1.06304 | 0.00269 | 8.0786 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(3415435..3415989) | matched_representative_sequence=group_3358 | BKLOHC_02860;HFPBEP_03965;JEBLOM_03441;LFDDMP_04197;LPCJNG_03538;NNCHJK_03916;ODNJBD_03549;OJHMIJ_03868 | hypothetical protein | |||
| 84 | group_23 | gene_presence_absence | Rv3136A (group_23) | group_23 | Rv3136A | high confidence | group_23 | hypothetical protein | Rv3136A | hypothetical protein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 1 | 50 | 0.0200 | 7 | 50 | 0.1400 | Check manually | 7.36 | 0.175758 | 0.02906-1.063 | 0.029059 | 1.06304 | 0.00269 | 8.0786 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | complement(3502945..3503277) | matched_representative_sequence=group_2370 | BKLOHC_02861;HFPBEP_03966;JEBLOM_03440;LFDDMP_04196;LPCJNG_03539;NNCHJK_03917;ODNJBD_03548;OJHMIJ_03867 | hypothetical protein | |||
| 85 | group_2760 | gene_presence_absence | PE_PGRS28 | group_2760 | Rv1452c | none confidence | PE_PGRS28 | hypothetical protein;PE domain-containing protein | Rv1452c | PE_PGRS28 | PE-PGRS family protein PE_PGRS28 | none | 91.64 | 27.73 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=91.64; coverage=27.73 | 46 | 50 | 0.9200 | 41 | 50 | 0.8200 | Check manually | -6.93 | 2.36546 | 0.7145-7.832 | 0.714472 | 7.83153 | 0.000146 | 8.0778 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(1636004..1638229) | matched_representative_sequence=group_2760 | AEDLOG_01045;AEMPHK_04100;AEMPHK_04101;AFKOAF_00125;AFNKCG_01027;ANMCAC_04051;APAKNA_04080;BDILPO_04073;BDMCKA_04072;BDMCKA_04073;BGEAED_01356;BHJHEC_04077;BHJHEC_04078;BPEJMN_04080;BPLIPK_04097;BPLIPK_04098;CBPCJH_04081;CIMEKD_04093;CKHCDK_04155;CKHCDK_04156;DBCCLE_04114;DJMHJN_02904;DNOEHN_04086;DNOEHN_04087;DOFGLF_04059;DPLIOB_04131;DPLIOB_04132;EBKMEK_03787;EEGMED_04159;EEMIBL_04107 | PE-PGRS family protein PE_PGRS28 | ||
| 86 | recD | gene_presence_absence | recD | recD | Rv0629c | high confidence | recD | RecBCD enzyme subunit RecD | Rv0629c | recD | exonuclease V subunit alpha RecD | high | 100.0 | 100.0 | High-confidence GenBank-supported annotation. | identity=100.0; coverage=100.0 | 49 | 50 | 0.9800 | 43 | 50 | 0.8600 | Check manually | -7.29 | 5.68966 | 0.9407-34.41 | 0.940703 | 34.4128 | 0.00279 | 8.0627 | Panaroo/Bakta+GenBank | qualifier_exact | complement(720005..721732) | 0_refound_11_pseudo;13_refound_527_pseudo;AEDLOG_00628;AEMPHK_00308;AFKOAF_02648;AFNKCG_02524;ANMCAC_00178;APAKNA_03712;BDILPO_01967;BDMCKA_00636;BGEAED_01509;BHJHEC_01305;BPEJMN_00332;BPLIPK_00909;CBPCJH_01209;CIMEKD_01323;CKHCDK_00118;DBCCLE_01971;DJMHJN_00749;DNOEHN_00854;DOFGLF_00276;DPLIOB_02793;EBKMEK_00984;EEGMED_02100;EEMIBL_00411;EOJHMN_02109;EPBFME_00579;FDDMPP_00375;FGOACM_00409;FLEJOH_02644 | exonuclease V subunit alpha RecD | |||
| 87 | group_1321 | gene_presence_absence | group_1321 | group_1321 | Rv3430c | none confidence | group_1321 | transposase | Rv3430c | transposase | none | 35.48 | 3.03 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=35.48; coverage=3.03 | 1 | 50 | 0.0200 | 7 | 50 | 0.1400 | Check manually | 7.29 | 0.175758 | 0.02906-1.063 | 0.029059 | 1.06304 | 0.00279 | 8.0627 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(3847642..3848805) | matched_representative_sequence=group_1321 | HFPBEP_02139;JEBLOM_02640;KBDFIK_03131;LPCJNG_02849;NJPOJP_02045;NNCHJK_02284;ODNJBD_02831;OJHMIJ_02212 | transposase | |||
| 88 | group_2851 | gene_presence_absence | group_2851 | group_2851 | Rv0804 | none confidence | group_2851 | hypothetical protein | Rv0804 | hypothetical protein | none | 32.82 | 10.26 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=32.82; coverage=10.26 | 10 | 50 | 0.2000 | 36 | 50 | 0.7200 | controls (rpoB 763031 T C absent) | -1.48 | 0.102993 | 0.04139-0.2563 | 0.0413935 | 0.256264 | 0.0182 | 8.0193 | Panaroo/Bakta+GenBank | nucleotide_similarity | 898081..898710 | matched_representative_sequence=21_refound_872 | 21_refound_872;98_refound_2450;AEDLOG_04109;BDMCKA_04121;BGEAED_04131;BHJHEC_04122;BPLIPK_04145;CBPCJH_04121;CKHCDK_04176;DBCCLE_04116;DOFGLF_02699;DPLIOB_04172;EEGMED_04183;EEMIBL_04135;FLEJOH_03643;FNLDAG_04203;FOMADB_04119;GKLDEJ_03127;HFPBEP_04085;HIHJDO_04320;HLEDKO_04122;ICLPCH_04098;IJKJHL_01948;ILFCIO_04171;IPDLAB_04141;JEBLOM_04183;JFHJPL_04086;JFNAAB_03020;JGDOPI_04214;KBDFIK_04128 | hypothetical protein | |||
| 89 | group_3103 | gene_presence_absence | PE_PGRS48-like (group_3103) | group_3103 | Rv2853 | low confidence | PE_PGRS48 | PE-PGRS family protein PE_PGRS48 | Rv2853 | PE_PGRS48 | PE-PGRS family protein PE_PGRS48 | low | 99.46 | 53.27 | Low-confidence GenBank rescue; treat as tentative and keep the Panaroo cluster ID. | identity=99.46; coverage=53.27 | 48 | 50 | 0.9600 | 43 | 50 | 0.8600 | Check manually | -7.3 | 3.34483 | 0.7548-14.82 | 0.754776 | 14.8228 | 0.000546 | 8.0047 | Panaroo/Bakta+GenBank | nucleotide_similarity | 3162268..3164115 | matched_representative_sequence=group_3103 | AEDLOG_03361;AEMPHK_03156;AFKOAF_03680;AFNKCG_02276;AFNKCG_02450;ANMCAC_03258;APAKNA_01881;BDILPO_02972;BDMCKA_03815;BGEAED_01110;BHJHEC_03826;BKLOHC_04242;BPEJMN_03546;BPLIPK_03973;CBPCJH_00804;CIMEKD_02934;CKHCDK_03202;CKHCDK_03291;CKHCDK_04170;DBCCLE_03864;DJMHJN_02458;DNOEHN_02382;DOFGLF_03896;DPLIOB_02912;EBKMEK_00035;EEGMED_03049;EEGMED_03998;EEMIBL_02723;EOJHMN_03217;EPBFME_02245 | PE-PGRS family protein PE_PGRS48 | ||
| 90 | group_439 | gene_presence_absence | Rv1817 (group_439) | group_439 | Rv1817 | high confidence | group_439 | FAD-dependent oxidoreductase 2 FAD binding domain-containing protein | Rv1817 | flavoprotein | high | 100.00 | 100.00 | High-confidence locus-level GenBank rescue. | identity=100.00; coverage=100.00 | 49 | 50 | 0.9800 | 44 | 50 | 0.8800 | Check manually | -8.18 | 4.82022 | 0.7802-29.78 | 0.780225 | 29.7793 | 0.00187 | 7.9973 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 2059595..2061058 | matched_representative_sequence=group_439 | AEDLOG_03893;AEMPHK_01455;AFKOAF_01385;AFNKCG_03496;ANMCAC_01482;APAKNA_00960;BDILPO_01782;BDMCKA_02627;BGEAED_02389;BHJHEC_02883;BPEJMN_01721;BPLIPK_02933;CBPCJH_01386;CIMEKD_01172;CKHCDK_03808;DBCCLE_03566;DJMHJN_01262;DNOEHN_02631;DOFGLF_01366;DPLIOB_03818;EBKMEK_03827;EEGMED_03345;EEMIBL_02006;EOJHMN_03281;EPBFME_01281;FDDMPP_00974;FGOACM_03514;FLEJOH_03893;FNACPH_01545;FNLDAG_04131 | flavoprotein | |||
| 91 | group_1310 | gene_presence_absence | hycE | group_1310 | Rv0087 | high confidence | hycE | formate hydrogenase HycE | Rv0087 | hycE | formate hydrogenase HycE | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 42 | 50 | 0.8400 | 16 | 50 | 0.3200 | cases (rpoB 763031 T C present) | 1.36 | 10.4545 | 4.078-26.8 | 4.07751 | 26.805 | 0.0273 | 7.9499 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 95414..96892 | matched_representative_sequence=0_refound_93 | 0_refound_93;13_refound_582_pseudo;95_refound_2363_pseudo;AEDLOG_00570;AEMPHK_02223;AFNKCG_03438;ANMCAC_02597;APAKNA_00116;BGEAED_00385;BPEJMN_02951;CIMEKD_01991;DBCCLE_01453;DJMHJN_03458;DNOEHN_01838;DPLIOB_00726;EBKMEK_02321;EEMIBL_01559;EOJHMN_01523;EPBFME_02414;FDDMPP_03213;FLEJOH_00575;FNACPH_02596;GNKHBM_01027;HEJICF_02156;HLIGOK_00216;HNJHNP_02170;IDADDB_01002;IEDNOI_01940;IJGDKF_00789;IJKJHL_01716 | formate hydrogenase HycE | ||
| 92 | group_2820 | gene_presence_absence | PE_PGRS15-like | group_2820 | Rv0872c | medium confidence | PE_PGRS15 | hypothetical protein;PE family protein | Rv0872c | PE_PGRS15 | PE-PGRS family protein PE_PGRS15 | medium | 99.70 | 72.95 | Medium-confidence GenBank rescue; inspect manually before biological interpretation. | identity=99.70; coverage=72.95 | 48 | 50 | 0.9600 | 41 | 50 | 0.8200 | Check manually | -7.27 | 4.44096 | 1.038-19 | 1.03803 | 18.9996 | 0.00177 | 7.9029 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(968424..970244) | matched_representative_sequence=group_2820 | 2_refound_190_pseudo;38_refound_1084_pseudo;AEDLOG_00946;AEMPHK_00688;AFKOAF_03749;AFNKCG_01862;ANMCAC_01267;APAKNA_02425;BDILPO_01923;BDMCKA_03399;BGEAED_04029;BHJHEC_01555;BKLOHC_03626;BPEJMN_00705;BPLIPK_00744;CBPCJH_03954;CIMEKD_00655;CKHCDK_04086;DBCCLE_00764;DJMHJN_00449;DNOEHN_02071;DOFGLF_03957;DPLIOB_03999;EBKMEK_00818;EEGMED_04099;EEMIBL_01802;EOJHMN_03870;EPBFME_01448;FDDMPP_00913;FGOACM_02884 | PE-PGRS family protein PE_PGRS15 | ||
| 93 | group_1398 | gene_presence_absence | group_1398 | group_1398 | Rv3851 | none confidence | group_1398 | membrane protein | Rv3851 | membrane protein | none | 42.61 | 5.05 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=42.61; coverage=5.05 | 2 | 50 | 0.0400 | 9 | 50 | 0.1800 | Check manually | 7.27 | 0.225176 | 0.05263-0.9634 | 0.0526327 | 0.963363 | 0.00177 | 7.9029 | Panaroo/Bakta+GenBank | nucleotide_similarity | 4324683..4324967 | matched_representative_sequence=group_1398 | 12_refound_494_pseudo;22_refound_887_pseudo;40_refound_1246_pseudo;94_refound_2274_pseudo;FOMADB_03732;JEBLOM_02486;LFDDMP_03233;LPCJNG_03580;NJPOJP_02993;NNCHJK_03087;ODNJBD_02712 | membrane protein | |||
| 94 | group_864 | gene_presence_absence | group_864 | group_864 | Rv2957 | none confidence | group_864 | PGL/p-HBAD biosynthesis glycosyltransferase | Rv2957 | PGL/p-HBAD biosynthesis glycosyltransferase | none | 14.26 | 2.33 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=14.26; coverage=2.33 | 2 | 50 | 0.0400 | 8 | 50 | 0.1600 | Check manually | 7.79 | 0.257732 | 0.05931-1.12 | 0.0593138 | 1.1199 | 0.00116 | 7.8916 | Panaroo/Bakta+GenBank | nucleotide_similarity | 3309470..3310297 | matched_representative_sequence=group_864 | HFPBEP_03600;HIHJDO_03233;JEBLOM_02307;KBDFIK_03272;LFDDMP_02033;LPCJNG_02572;NJPOJP_03500;NNCHJK_03614;ODNJBD_02620;OJHMIJ_03561 | PGL/p-HBAD biosynthesis glycosyltransferase | |||
| 95 | group_632 | gene_presence_absence | idsA2 | group_632 | Rv2173 | none confidence | idsA2 | geranylgeranyl pyrophosphate synthetase IdsA | Rv2173 | idsA2 | geranylgeranyl pyrophosphate synthetase IdsA | none | 38.11 | 2.53 | Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. | identity=38.11; coverage=2.53 | 2 | 50 | 0.0400 | 8 | 50 | 0.1600 | Check manually | 7.79 | 0.257732 | 0.05931-1.12 | 0.0593138 | 1.1199 | 0.00116 | 7.8916 | Panaroo/Bakta+GenBank | nucleotide_similarity | 2434847..2435905 | matched_representative_sequence=group_632 | BKLOHC_01290;HFPBEP_01829;HIHJDO_02819;JEBLOM_01658;LFDDMP_01228;LPCJNG_00933;NJPOJP_02479;NNCHJK_01832;ODNJBD_00907;OJHMIJ_02589 | geranylgeranyl pyrophosphate synthetase IdsA | ||
| 96 | group_3067 | gene_presence_absence | PE_PGRS33-like (group_3067) | group_3067 | Rv1818c | low confidence | PE_PGRS33 | PE-PGRS family protein PE_PGRS33 | Rv1818c | PE_PGRS33 | PE-PGRS family protein PE_PGRS33 | low | 99.63 | 47.54 | Low-confidence GenBank rescue; treat as tentative and keep the Panaroo cluster ID. | identity=99.63; coverage=47.54 | 46 | 50 | 0.9200 | 39 | 50 | 0.7800 | Check manually | -5.08 | 3.00844 | 0.9342-9.688 | 0.934234 | 9.68783 | 0.000518 | 7.8747 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(2061178..2062674) | matched_representative_sequence=group_3067 | 19_refound_796_pseudo;1_refound_173_pseudo;2_refound_195_pseudo;36_refound_1057_pseudo;38_refound_1088_pseudo;42_refound_1365_pseudo;62_refound_1732_pseudo;64_refound_1783_pseudo;67_refound_1823_pseudo;82_refound_2098_pseudo;91_refound_2220_pseudo;92_refound_2240_pseudo;AEDLOG_03892;AEMPHK_01454;AFKOAF_01386;ANMCAC_01481;APAKNA_00959;BDILPO_01781;BDMCKA_02626;BGEAED_02388;BPEJMN_01720;BPLIPK_02932;CBPCJH_01385;CIMEKD_01171;CKHCDK_03807;DJMHJN_01263;DOFGLF_01367;DPLIOB_03817;EEGMED_03344;EEMIBL_02005 | PE-PGRS family protein PE_PGRS33 | ||
| 97 | group_3435 | gene_presence_absence | group_3435 | group_3435 | Rv1580c | none confidence | group_3435 | phage protein | Rv1580c | phage protein | none | 39.63 | 3.16 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=39.63; coverage=3.16 | 1 | 50 | 0.0200 | 6 | 50 | 0.1200 | Check manually | 7.29 | 0.207459 | 0.03358-1.282 | 0.0335803 | 1.28168 | 0.00278 | 7.8251 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(1783620..1783892) | matched_representative_sequence=group_3435 | BKLOHC_04166;HFPBEP_04147;LPCJNG_04155;NJPOJP_04104;NNCHJK_04150;ODNJBD_04145;OJHMIJ_04122 | phage protein | |||
| 98 | group_3093 | gene_presence_absence | PE_PGRS2 | group_3093 | Rv0124 | high confidence | PE_PGRS2 | hypothetical protein;PE domain-containing protein | Rv0124 | PE_PGRS2 | PE-PGRS family protein PE_PGRS2 | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 41 | 50 | 0.8200 | 32 | 50 | 0.6400 | Check manually | -3.38 | 2.48664 | 1.004-6.16 | 1.00385 | 6.15964 | 0.000313 | 7.8187 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 149533..150996 | matched_representative_sequence=37_refound_1068 | 14_refound_636_pseudo;2_refound_196_pseudo;36_refound_1059_pseudo;37_refound_1068;38_refound_1089;42_refound_1366_pseudo;45_refound_1482;69_refound_1862;96_refound_2424_pseudo;AEMPHK_00484;AFKOAF_02199;ANMCAC_00464;APAKNA_00081;BDILPO_00218;BGEAED_01716;BHJHEC_01182;BPEJMN_00221;BPLIPK_00705;CBPCJH_02271;CIMEKD_00164;DJMHJN_00163;DNOEHN_00567;DOFGLF_00031;EBKMEK_00371;EEGMED_03136;EEMIBL_00748;EOJHMN_03473;EPBFME_00425;FDDMPP_00223;FGOACM_01327 | PE-PGRS family protein PE_PGRS2 | ||
| 99 | group_857 | gene_presence_absence | group_857 | group_857 | Rv0371c | none confidence | group_857 | hypothetical protein | Rv0371c | hypothetical protein | none | 18.44 | 3.12 | No confident reference gene assignment; report the stable Panaroo cluster ID. | identity=18.44; coverage=3.12 | 1 | 50 | 0.0200 | 11 | 50 | 0.2200 | Check manually | 4.57 | 0.104084 | 0.01805-0.6002 | 0.0180485 | 0.600245 | 0.0308 | 7.7756 | Panaroo/Bakta+GenBank | nucleotide_similarity | complement(448040..448633) | matched_representative_sequence=group_857 | BKLOHC_04041;FNLDAG_03841;FOMADB_04073;HFPBEP_04093;JEBLOM_03871;LFDDMP_03768;LPCJNG_03949;NGOKMK_03215;NJPOJP_04051;NNCHJK_04103;ODNJBD_03930;OJHMIJ_04053 | hypothetical protein | |||
| 100 | group_301 | gene_presence_absence | rpsT | group_301 | Rv2412 | high confidence | rpsT | 30S ribosomal protein S20 | Rv2412 | rpsT | 30S ribosomal protein S20 | high | 100.00 | 100.00 | High-confidence GenBank-supported annotation. | identity=100.00; coverage=100.00 | 1 | 50 | 0.0200 | 11 | 50 | 0.2200 | Check manually | 4.57 | 0.104084 | 0.01805-0.6002 | 0.0180485 | 0.600245 | 0.0308 | 7.7756 | Panaroo/Bakta+GenBank | nucleotide_exact_or_contained | 2710075..2710335 | matched_representative_sequence=group_3011 | BKLOHC_04040;FNLDAG_03840;FOMADB_04074;HFPBEP_04092;JEBLOM_03872;LFDDMP_03769;LPCJNG_03950;NGOKMK_03214;NJPOJP_04052;NNCHJK_04102;ODNJBD_03929;OJHMIJ_04054 | 30S ribosomal protein S20 |
Showing 100 of 178 rows.
| Confidence | Rule | Interpretation |
|---|---|---|
| high | >=95% identity and >=90% coverage, or exact qualifier-level support | Strong reference-supported annotation |
| medium | >=85% identity and >=70% coverage | Plausible annotation; inspect manually |
| low | >=60% identity and >=50% coverage, or weak/partial support | Tentative annotation only |
| none | No usable GenBank match | Keep the pangenome/SNP marker identifier |
metric value reference_cds_parsed 3906 reference_parse_warning panaroo_clusters_parsed 4348 annotation_engine Panaroo/Bakta fasta_records_parsed 419405 top_priority_input MTB_rpoB_763031_44v44_marker_validation_top_priority_hits.tsv all_significant_input MTB_rpoB_763031_44v44_marker_validation_all_significant_hits.tsv method GenBank qualifier matching plus pure-Python nucleotide similarity rescue when Panaroo representative sequences are available
rMAP-GWAS sample-set input validation report ================================================ Cases (rpoB 763031 T C present): 50 Controls (rpoB 763031 T C absent): 50 Total samples: 100 Case (rpoB 763031 T C present) label: case (rpoB 763031 T C present) Control (rpoB 763031 T C absent) label: control (rpoB 763031 T C absent) Phenotype display metadata values provided: yes Unique phenotype display values: rpoB_763031_T_C_absent, rpoB_763031_T_C_present Status: PASS
Panaroo output files: panaroo_out/combined_DNA_CDS.fasta panaroo_out/combined_protein_CDS.fasta panaroo_out/combined_protein_cdhit_out.txt panaroo_out/combined_protein_cdhit_out.txt.clstr panaroo_out/final_graph.gml panaroo_out/gene_data.csv panaroo_out/gene_presence_absence.Rtab panaroo_out/gene_presence_absence.csv panaroo_out/gene_presence_absence_roary.csv panaroo_out/pan_genome_reference.fa panaroo_out/pre_filt_graph.gml panaroo_out/struct_presence_absence.Rtab panaroo_out/summary_statistics.txt
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