Cromwell workflow report

rMAP-GWAS

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.

CromwellDockerizedDistance-corrected pyseerMulti-pathogen readyExplicit phenotype codingAMR interpretation guardrailsGenBank annotation rescueOptional SNP GWAS
GWAS phenotype being tested: This run tests one explicitly configured binary phenotype only: MSSA_vs_MRSA. The biological contrast used by the model is case (MRSA) versus control (MSSA). For AMR analyses, configure the input metadata so that phenotypically resistant isolates are case=1 and susceptible isolates are control=0.
Association scope: General guardrail, especially for AMR use cases: Association results should be interpreted as statistical marker-phenotype associations, not as final clinical resistance calls. Gene presence/absence is the primary marker set; optional SNP GWAS adds point-mutation markers. Sequencing depth, assembly quality, species background, multiple genes in the same antibiotic class, plasmid linkage, and phenotype quality should be reviewed during filtering and interpretation.
Sample-size interpretation note: This run has 100 samples (50 cases (MRSA) and 50 controls (MSSA)). Interpret association strength in relation to cohort size, phenotype balance, population structure, and independent validation before making biological, clinical, or public-health claims.
cases (MRSA)
50
controls (MSSA)
50
Total samples
100
Top gene hit
group_8632
group_8632 | SAOUHSC_00003 | none confidence | identity=42.51% | coverage=4.17%
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01 Phenotype legend and coding

Brief interpretation: This section confirms the exact binary contrast used by pyseer: case (MRSA) is coded as 1 and control (MSSA) is coded as 0. Confirm that these labels match the study metadata before interpreting associations.
Phenotype tested: Binary phenotype MSSA_vs_MRSA. Configured contrast: case (MRSA) versus control (MSSA). The report displays the metadata-derived biological contrast throughout the HTML: case (MRSA) = 1 and control (MSSA) = 0.
ClassPyseer codingMetadata columnMetadata value used for displaySamplesReport label
case1MSSA_vs_MRSAMRSA50case (MRSA)
control0MSSA_vs_MRSAMSSA50control (MSSA)
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01b AMR phenotype and association scope

Brief interpretation: This section addresses AMR-specific interpretation concerns: resistance versus susceptibility coding, species background, depth and assembly quality, SNP/point mutations, and co-occurring resistance genes for the case (MRSA) versus control (MSSA) contrast.
Configured phenotype: This run tests one explicitly configured binary phenotype only: MSSA_vs_MRSA. The biological contrast used by the model is case (MRSA) versus control (MSSA). For AMR analyses, configure the input metadata so that phenotypically resistant isolates are case=1 and susceptible isolates are control=0.
Interpretation issueCurrent workflow/report behaviorRecommended AMR interpretation
Phenotype clarityOne binary phenotype is tested per run using the phenotype TSV supplied to pyseer.For AMR, label the contrast explicitly as phenotypically resistant versus susceptible and verify case/control coding before launch.
Gene presence/absenceThe primary GWAS branch tests pangenome gene-cluster presence/absence with population-structure correction.A resistance gene found in some susceptible isolates may reflect gene inactivity, expression differences, breakpoint issues, linkage, or phenotype error; interpret enrichment rather than presence alone.
Point mutationsPoint mutations are not represented by gene presence/absence; they are assessed only when the optional SNP GWAS branch is enabled.Use do_snp_gwas=true for mutation-mediated resistance, such as many MTBC drug-resistance phenotypes, and interpret SNP hits alongside known resistance catalogs where available.
Species backgroundSpecies labels are recorded as run provenance, but species is not automatically included as a regression covariate in the default model.Avoid pooling divergent species without review. Prefer species-specific or lineage-aware analyses when associations may differ by species.
Sequencing depth and assembly qualityThe 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 inspect gene absence in susceptible/resistant groups before making biological claims.
Multiple resistance genes in the same classPrioritized hits are marker-level associations and may be correlated through plasmids, mobile elements, clonal background, or co-carriage.For antibiotic-class interpretation, inspect gene co-occurrence and consider class-level summaries or follow-up multivariable models outside this summary report.
Population structure and linkageMash distances/MDS and population-structure plots are generated to help assess lineage confounding.If resistant and susceptible isolates cluster by lineage or outbreak, treat hits as candidates requiring validation rather than causal resistance determinants.
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02 Workflow architecture

Brief interpretation: Reads are quality-trimmed, assembled, annotated with Bakta, summarized as a Panaroo pangenome, tested with pyseer, and then annotated against the selected reference package.
01
Input
Sample-set validation

Checks sample names, paired FASTQs, group labels, and case (MRSA)/control (MSSA) balance.

02
QC
fastp trimming

Generates cleaned reads plus QC summaries.

03
Assembly
Shovill

Builds de novo genome assemblies using safe Cromwell memory handling.

04
Annotation
Bakta + Panaroo

Creates GFF annotations and pangenome gene matrices. Prokka remains the default; Bakta can be enabled with use_bakta=true.

05
GWAS
Mash + pyseer

Runs population-structure-aware gene and optional SNP association testing.

06
Rescue
GenBank annotation

Maps prioritized pangenome/SNP markers to reference GenBank features where possible.

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03 Run configuration

Brief interpretation: The report records the reference package, species label, annotation engine, GWAS mode, SNP branch, Gubbins status, and container backend so that the run can be audited and repeated.
Reference name
SAUREUS_2026_06
Species
Staphylococcus aureus
Reference Docker
gmboowa/rmap-gwas-saureus-refs:2026.06
Generated UTC
2026-07-01T08:22:56Z
Phenotype coding: case (MRSA) = 1; control (MSSA) = 0. GWAS mode: gene_presence_absence_plus_snp; SNP branch: run; Gubbins recombination module: not run; annotation engine: Bakta; container backend recorded as docker.
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04 Top-hit GenBank annotation rescue

Brief interpretation: The top gene hit is a candidate association for the case (MRSA) versus control (MSSA) contrast. Treat it as a hypothesis until supported by sample size, population-structure checks, annotation confidence, and independent validation.
Display name
group_8632
Pangenome/SNP marker
group_8632
Reference locus / gene
SAOUHSC_00003 / not assigned
Confidence
none
Top-hit interpretation: No confident reference gene assignment; report the stable Panaroo cluster ID. Reference identity: 42.51%; reference coverage: 4.17%. Product: hypothetical protein.
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05 Population structure

Brief interpretation: The PCoA plot shows moderate separation between the two phenotype groups (PCoA separation score 0.73; between/within Mash distance ratio 1.22). Some GWAS signals may still be influenced by lineage, so prioritize hits that remain biologically plausible and are not explained only by clustering.
Interpretation check: Review case (MRSA)/control (MSSA) clustering before interpreting top hits. Strong phenotype-lineage clustering can indicate lineage-associated markers rather than causal phenotype-associated variation.
Lay interpretation — PCoA: The PCoA plot shows moderate separation between the two phenotype groups (PCoA separation score 0.73; between/within Mash distance ratio 1.22). Some GWAS signals may still be influenced by lineage, so prioritize hits that remain biologically plausible and are not explained only by clustering.
Population structure: Mash PCoA ERR11728851 (control (MSSA)) ERR11728852 (control (MSSA)) ERR11728855 (control (MSSA)) ERR11728856 (control (MSSA)) ERR11728857 (control (MSSA)) ERR11728858 (control (MSSA)) ERR11728860 (control (MSSA)) ERR11728862 (control (MSSA)) ERR11728863 (control (MSSA)) ERR11728864 (control (MSSA)) ERR11728865 (control (MSSA)) ERR11728866 (control (MSSA)) ERR11728867 (case (MRSA)) ERR11728869 (control (MSSA)) ERR11728871 (control (MSSA)) ERR11728872 (control (MSSA)) ERR11728873 (control (MSSA)) ERR11728874 (control (MSSA)) ERR11728875 (control (MSSA)) ERR11728877 (control (MSSA)) ERR11728879 (control (MSSA)) ERR11728881 (control (MSSA)) ERR11728882 (control (MSSA)) ERR11728884 (control (MSSA)) ERR11728885 (control (MSSA)) ERR11728888 (case (MRSA)) ERR11728891 (control (MSSA)) ERR11728892 (case (MRSA)) ERR11728894 (control (MSSA)) ERR11728895 (control (MSSA)) ERR11728896 (control (MSSA)) ERR11728897 (control (MSSA)) ERR11728898 (control (MSSA)) ERR11728899 (control (MSSA)) ERR11728900 (control (MSSA)) ERR11728901 (control (MSSA)) ERR11728902 (control (MSSA)) ERR11728903 (control (MSSA)) ERR11728904 (control (MSSA)) ERR11728905 (case (MRSA)) ERR11728906 (control (MSSA)) ERR11728908 (control (MSSA)) ERR11728909 (control (MSSA)) ERR11728910 (case (MRSA)) ERR11728911 (control (MSSA)) ERR11728912 (case (MRSA)) ERR11728913 (case (MRSA)) ERR11728916 (control (MSSA)) ERR11728917 (control (MSSA)) ERR11728918 (case (MRSA)) ERR11728919 (control (MSSA)) ERR11728920 (control (MSSA)) ERR11728922 (control (MSSA)) ERR11728923 (control (MSSA)) ERR11728924 (control (MSSA)) ERR11728925 (control (MSSA)) ERR11728926 (case (MRSA)) ERR11728927 (case (MRSA)) ERR11728928 (case (MRSA)) ERR11728930 (case (MRSA)) ERR11728932 (case (MRSA)) ERR11728933 (case (MRSA)) ERR11728934 (case (MRSA)) ERR11728935 (case (MRSA)) ERR11728936 (case (MRSA)) ERR11728938 (case (MRSA)) ERR11728940 (case (MRSA)) ERR11728942 (case (MRSA)) ERR11728943 (case (MRSA)) ERR11728945 (case (MRSA)) ERR11728946 (case (MRSA)) ERR11728948 (control (MSSA)) ERR11728949 (case (MRSA)) ERR11728951 (case (MRSA)) ERR11728952 (case (MRSA)) ERR11728953 (case (MRSA)) ERR11728954 (case (MRSA)) ERR11728955 (case (MRSA)) ERR11728956 (case (MRSA)) ERR11728957 (case (MRSA)) ERR11728959 (case (MRSA)) ERR11728960 (case (MRSA)) ERR11728961 (case (MRSA)) ERR11728962 (case (MRSA)) ERR11728966 (case (MRSA)) ERR11728969 (case (MRSA)) ERR11728970 (case (MRSA)) ERR11728971 (case (MRSA)) ERR11728974 (case (MRSA)) ERR11728975 (case (MRSA)) ERR11728976 (case (MRSA)) ERR11728977 (case (MRSA)) ERR11728978 (case (MRSA)) ERR11728979 (case (MRSA)) ERR11728981 (case (MRSA)) ERR11728982 (control (MSSA)) ERR11728983 (case (MRSA)) ERR11728984 (case (MRSA)) ERR11728985 (case (MRSA)) ERR11728986 (case (MRSA)) case (MRSA) control (MSSA) PCoA1 (59.9% variance) PCoA2 (17.9% variance)
Mash distance / kinship matrix ERR11728851 vs ERR11728851 ERR11728851 vs ERR11728852 ERR11728851 vs ERR11728855 ERR11728851 vs ERR11728856 ERR11728851 vs ERR11728857 ERR11728851 vs ERR11728858 ERR11728851 vs ERR11728860 ERR11728851 vs ERR11728862 ERR11728851 vs ERR11728863 ERR11728851 vs ERR11728864 ERR11728851 vs ERR11728865 ERR11728851 vs ERR11728866 ERR11728851 vs ERR11728869 ERR11728851 vs ERR11728871 ERR11728851 vs ERR11728872 ERR11728851 vs ERR11728873 ERR11728851 vs ERR11728874 ERR11728851 vs ERR11728875 ERR11728851 vs ERR11728877 ERR11728851 vs ERR11728879 ERR11728851 vs ERR11728881 ERR11728851 vs ERR11728882 ERR11728851 vs ERR11728884 ERR11728851 vs ERR11728885 ERR11728851 vs ERR11728891 ERR11728851 vs ERR11728894 ERR11728851 vs ERR11728895 ERR11728851 vs ERR11728896 ERR11728851 vs ERR11728897 ERR11728851 vs ERR11728898 ERR11728851 vs ERR11728899 ERR11728851 vs ERR11728900 ERR11728851 vs ERR11728901 ERR11728851 vs ERR11728902 ERR11728851 vs ERR11728903 ERR11728851 vs ERR11728904 ERR11728851 vs ERR11728906 ERR11728851 vs ERR11728908 ERR11728851 vs ERR11728909 ERR11728851 vs ERR11728911 ERR11728851 vs ERR11728916 ERR11728851 vs ERR11728917 ERR11728851 vs ERR11728919 ERR11728851 vs ERR11728920 ERR11728851 vs ERR11728922 ERR11728851 vs ERR11728923 ERR11728851 vs ERR11728924 ERR11728851 vs ERR11728925 ERR11728851 vs ERR11728948 ERR11728851 vs ERR11728982 ERR11728851 vs ERR11728867 ERR11728851 vs ERR11728888 ERR11728851 vs ERR11728892 ERR11728851 vs ERR11728905 ERR11728851 vs ERR11728910 ERR11728851 vs ERR11728912 ERR11728851 vs ERR11728913 ERR11728851 vs ERR11728918 ERR11728851 vs ERR11728926 ERR11728851 vs ERR11728927 ERR11728851 vs ERR11728928 ERR11728851 vs ERR11728930 ERR11728851 vs ERR11728932 ERR11728851 vs ERR11728933 ERR11728851 vs ERR11728934 ERR11728851 vs ERR11728935 ERR11728851 vs ERR11728936 ERR11728851 vs ERR11728938 ERR11728851 vs ERR11728940 ERR11728851 vs ERR11728942 ERR11728851 vs ERR11728943 ERR11728851 vs ERR11728945 ERR11728851 vs ERR11728946 ERR11728851 vs ERR11728949 ERR11728851 vs ERR11728951 ERR11728851 vs ERR11728952 ERR11728851 vs ERR11728953 ERR11728851 vs ERR11728954 ERR11728851 vs ERR11728955 ERR11728851 vs ERR11728956 ERR11728851 vs ERR11728957 ERR11728851 vs ERR11728959 ERR11728851 vs ERR11728960 ERR11728851 vs ERR11728961 ERR11728851 vs ERR11728962 ERR11728851 vs ERR11728966 ERR11728851 vs ERR11728969 ERR11728851 vs ERR11728970 ERR11728851 vs ERR11728971 ERR11728851 vs ERR11728974 ERR11728851 vs ERR11728975 ERR11728851 vs ERR11728976 ERR11728851 vs ERR11728977 ERR11728851 vs ERR11728978 ERR11728851 vs ERR11728979 ERR11728851 vs ERR11728981 ERR11728851 vs ERR11728983 ERR11728851 vs ERR11728984 ERR11728851 vs ERR11728985 ERR11728851 vs ERR11728986 ERR11728852 vs ERR11728851 ERR11728852 vs ERR11728852 ERR11728852 vs ERR11728855 ERR11728852 vs ERR11728856 ERR11728852 vs ERR11728857 ERR11728852 vs ERR11728858 ERR11728852 vs ERR11728860 ERR11728852 vs ERR11728862 ERR11728852 vs ERR11728863 ERR11728852 vs ERR11728864 ERR11728852 vs ERR11728865 ERR11728852 vs ERR11728866 ERR11728852 vs ERR11728869 ERR11728852 vs ERR11728871 ERR11728852 vs ERR11728872 ERR11728852 vs ERR11728873 ERR11728852 vs ERR11728874 ERR11728852 vs ERR11728875 ERR11728852 vs ERR11728877 ERR11728852 vs ERR11728879 ERR11728852 vs ERR11728881 ERR11728852 vs ERR11728882 ERR11728852 vs ERR11728884 ERR11728852 vs ERR11728885 ERR11728852 vs ERR11728891 ERR11728852 vs ERR11728894 ERR11728852 vs ERR11728895 ERR11728852 vs ERR11728896 ERR11728852 vs ERR11728897 ERR11728852 vs ERR11728898 ERR11728852 vs ERR11728899 ERR11728852 vs ERR11728900 ERR11728852 vs ERR11728901 ERR11728852 vs ERR11728902 ERR11728852 vs ERR11728903 ERR11728852 vs ERR11728904 ERR11728852 vs ERR11728906 ERR11728852 vs ERR11728908 ERR11728852 vs ERR11728909 ERR11728852 vs ERR11728911 ERR11728852 vs ERR11728916 ERR11728852 vs ERR11728917 ERR11728852 vs ERR11728919 ERR11728852 vs ERR11728920 ERR11728852 vs ERR11728922 ERR11728852 vs ERR11728923 ERR11728852 vs ERR11728924 ERR11728852 vs ERR11728925 ERR11728852 vs ERR11728948 ERR11728852 vs ERR11728982 ERR11728852 vs ERR11728867 ERR11728852 vs ERR11728888 ERR11728852 vs ERR11728892 ERR11728852 vs ERR11728905 ERR11728852 vs ERR11728910 ERR11728852 vs ERR11728912 ERR11728852 vs ERR11728913 ERR11728852 vs ERR11728918 ERR11728852 vs ERR11728926 ERR11728852 vs ERR11728927 ERR11728852 vs ERR11728928 ERR11728852 vs ERR11728930 ERR11728852 vs ERR11728932 ERR11728852 vs ERR11728933 ERR11728852 vs ERR11728934 ERR11728852 vs ERR11728935 ERR11728852 vs ERR11728936 ERR11728852 vs ERR11728938 ERR11728852 vs ERR11728940 ERR11728852 vs ERR11728942 ERR11728852 vs ERR11728943 ERR11728852 vs ERR11728945 ERR11728852 vs ERR11728946 ERR11728852 vs ERR11728949 ERR11728852 vs ERR11728951 ERR11728852 vs ERR11728952 ERR11728852 vs ERR11728953 ERR11728852 vs ERR11728954 ERR11728852 vs ERR11728955 ERR11728852 vs ERR11728956 ERR11728852 vs ERR11728957 ERR11728852 vs ERR11728959 ERR11728852 vs ERR11728960 ERR11728852 vs ERR11728961 ERR11728852 vs ERR11728962 ERR11728852 vs ERR11728966 ERR11728852 vs ERR11728969 ERR11728852 vs ERR11728970 ERR11728852 vs ERR11728971 ERR11728852 vs ERR11728974 ERR11728852 vs ERR11728975 ERR11728852 vs ERR11728976 ERR11728852 vs ERR11728977 ERR11728852 vs ERR11728978 ERR11728852 vs ERR11728979 ERR11728852 vs ERR11728981 ERR11728852 vs ERR11728983 ERR11728852 vs ERR11728984 ERR11728852 vs ERR11728985 ERR11728852 vs ERR11728986 ERR11728855 vs ERR11728851 ERR11728855 vs ERR11728852 ERR11728855 vs ERR11728855 ERR11728855 vs ERR11728856 ERR11728855 vs ERR11728857 ERR11728855 vs ERR11728858 ERR11728855 vs ERR11728860 ERR11728855 vs ERR11728862 ERR11728855 vs ERR11728863 ERR11728855 vs ERR11728864 ERR11728855 vs ERR11728865 ERR11728855 vs ERR11728866 ERR11728855 vs ERR11728869 ERR11728855 vs ERR11728871 ERR11728855 vs ERR11728872 ERR11728855 vs ERR11728873 ERR11728855 vs ERR11728874 ERR11728855 vs ERR11728875 ERR11728855 vs ERR11728877 ERR11728855 vs ERR11728879 ERR11728855 vs ERR11728881 ERR11728855 vs ERR11728882 ERR11728855 vs ERR11728884 ERR11728855 vs ERR11728885 ERR11728855 vs ERR11728891 ERR11728855 vs ERR11728894 ERR11728855 vs ERR11728895 ERR11728855 vs ERR11728896 ERR11728855 vs ERR11728897 ERR11728855 vs ERR11728898 ERR11728855 vs ERR11728899 ERR11728855 vs ERR11728900 ERR11728855 vs ERR11728901 ERR11728855 vs ERR11728902 ERR11728855 vs ERR11728903 ERR11728855 vs ERR11728904 ERR11728855 vs ERR11728906 ERR11728855 vs ERR11728908 ERR11728855 vs ERR11728909 ERR11728855 vs ERR11728911 ERR11728855 vs ERR11728916 ERR11728855 vs ERR11728917 ERR11728855 vs ERR11728919 ERR11728855 vs ERR11728920 ERR11728855 vs ERR11728922 ERR11728855 vs ERR11728923 ERR11728855 vs ERR11728924 ERR11728855 vs ERR11728925 ERR11728855 vs ERR11728948 ERR11728855 vs ERR11728982 ERR11728855 vs ERR11728867 ERR11728855 vs ERR11728888 ERR11728855 vs ERR11728892 ERR11728855 vs ERR11728905 ERR11728855 vs ERR11728910 ERR11728855 vs ERR11728912 ERR11728855 vs ERR11728913 ERR11728855 vs ERR11728918 ERR11728855 vs ERR11728926 ERR11728855 vs ERR11728927 ERR11728855 vs ERR11728928 ERR11728855 vs ERR11728930 ERR11728855 vs ERR11728932 ERR11728855 vs ERR11728933 ERR11728855 vs ERR11728934 ERR11728855 vs ERR11728935 ERR11728855 vs ERR11728936 ERR11728855 vs ERR11728938 ERR11728855 vs ERR11728940 ERR11728855 vs ERR11728942 ERR11728855 vs ERR11728943 ERR11728855 vs ERR11728945 ERR11728855 vs ERR11728946 ERR11728855 vs ERR11728949 ERR11728855 vs ERR11728951 ERR11728855 vs ERR11728952 ERR11728855 vs ERR11728953 ERR11728855 vs ERR11728954 ERR11728855 vs ERR11728955 ERR11728855 vs ERR11728956 ERR11728855 vs ERR11728957 ERR11728855 vs ERR11728959 ERR11728855 vs ERR11728960 ERR11728855 vs ERR11728961 ERR11728855 vs ERR11728962 ERR11728855 vs ERR11728966 ERR11728855 vs ERR11728969 ERR11728855 vs ERR11728970 ERR11728855 vs ERR11728971 ERR11728855 vs ERR11728974 ERR11728855 vs ERR11728975 ERR11728855 vs ERR11728976 ERR11728855 vs ERR11728977 ERR11728855 vs ERR11728978 ERR11728855 vs ERR11728979 ERR11728855 vs ERR11728981 ERR11728855 vs ERR11728983 ERR11728855 vs ERR11728984 ERR11728855 vs ERR11728985 ERR11728855 vs ERR11728986 ERR11728856 vs ERR11728851 ERR11728856 vs ERR11728852 ERR11728856 vs ERR11728855 ERR11728856 vs ERR11728856 ERR11728856 vs ERR11728857 ERR11728856 vs ERR11728858 ERR11728856 vs ERR11728860 ERR11728856 vs ERR11728862 ERR11728856 vs ERR11728863 ERR11728856 vs ERR11728864 ERR11728856 vs ERR11728865 ERR11728856 vs ERR11728866 ERR11728856 vs ERR11728869 ERR11728856 vs ERR11728871 ERR11728856 vs ERR11728872 ERR11728856 vs ERR11728873 ERR11728856 vs ERR11728874 ERR11728856 vs ERR11728875 ERR11728856 vs ERR11728877 ERR11728856 vs ERR11728879 ERR11728856 vs ERR11728881 ERR11728856 vs ERR11728882 ERR11728856 vs ERR11728884 ERR11728856 vs ERR11728885 ERR11728856 vs ERR11728891 ERR11728856 vs ERR11728894 ERR11728856 vs ERR11728895 ERR11728856 vs ERR11728896 ERR11728856 vs ERR11728897 ERR11728856 vs ERR11728898 ERR11728856 vs ERR11728899 ERR11728856 vs ERR11728900 ERR11728856 vs ERR11728901 ERR11728856 vs ERR11728902 ERR11728856 vs ERR11728903 ERR11728856 vs ERR11728904 ERR11728856 vs ERR11728906 ERR11728856 vs ERR11728908 ERR11728856 vs ERR11728909 ERR11728856 vs ERR11728911 ERR11728856 vs ERR11728916 ERR11728856 vs ERR11728917 ERR11728856 vs ERR11728919 ERR11728856 vs ERR11728920 ERR11728856 vs ERR11728922 ERR11728856 vs ERR11728923 ERR11728856 vs ERR11728924 ERR11728856 vs ERR11728925 ERR11728856 vs ERR11728948 ERR11728856 vs ERR11728982 ERR11728856 vs ERR11728867 ERR11728856 vs ERR11728888 ERR11728856 vs ERR11728892 ERR11728856 vs ERR11728905 ERR11728856 vs ERR11728910 ERR11728856 vs ERR11728912 ERR11728856 vs ERR11728913 ERR11728856 vs ERR11728918 ERR11728856 vs ERR11728926 ERR11728856 vs ERR11728927 ERR11728856 vs ERR11728928 ERR11728856 vs ERR11728930 ERR11728856 vs ERR11728932 ERR11728856 vs ERR11728933 ERR11728856 vs ERR11728934 ERR11728856 vs ERR11728935 ERR11728856 vs ERR11728936 ERR11728856 vs ERR11728938 ERR11728856 vs ERR11728940 ERR11728856 vs ERR11728942 ERR11728856 vs ERR11728943 ERR11728856 vs ERR11728945 ERR11728856 vs ERR11728946 ERR11728856 vs ERR11728949 ERR11728856 vs ERR11728951 ERR11728856 vs ERR11728952 ERR11728856 vs ERR11728953 ERR11728856 vs ERR11728954 ERR11728856 vs ERR11728955 ERR11728856 vs ERR11728956 ERR11728856 vs ERR11728957 ERR11728856 vs ERR11728959 ERR11728856 vs ERR11728960 ERR11728856 vs ERR11728961 ERR11728856 vs ERR11728962 ERR11728856 vs ERR11728966 ERR11728856 vs ERR11728969 ERR11728856 vs ERR11728970 ERR11728856 vs ERR11728971 ERR11728856 vs ERR11728974 ERR11728856 vs ERR11728975 ERR11728856 vs ERR11728976 ERR11728856 vs ERR11728977 ERR11728856 vs ERR11728978 ERR11728856 vs ERR11728979 ERR11728856 vs ERR11728981 ERR11728856 vs ERR11728983 ERR11728856 vs ERR11728984 ERR11728856 vs ERR11728985 ERR11728856 vs ERR11728986 ERR11728857 vs ERR11728851 ERR11728857 vs ERR11728852 ERR11728857 vs ERR11728855 ERR11728857 vs ERR11728856 ERR11728857 vs ERR11728857 ERR11728857 vs ERR11728858 ERR11728857 vs ERR11728860 ERR11728857 vs ERR11728862 ERR11728857 vs ERR11728863 ERR11728857 vs ERR11728864 ERR11728857 vs ERR11728865 ERR11728857 vs ERR11728866 ERR11728857 vs ERR11728869 ERR11728857 vs ERR11728871 ERR11728857 vs ERR11728872 ERR11728857 vs ERR11728873 ERR11728857 vs ERR11728874 ERR11728857 vs ERR11728875 ERR11728857 vs ERR11728877 ERR11728857 vs ERR11728879 ERR11728857 vs ERR11728881 ERR11728857 vs ERR11728882 ERR11728857 vs ERR11728884 ERR11728857 vs ERR11728885 ERR11728857 vs ERR11728891 ERR11728857 vs ERR11728894 ERR11728857 vs ERR11728895 ERR11728857 vs ERR11728896 ERR11728857 vs ERR11728897 ERR11728857 vs ERR11728898 ERR11728857 vs ERR11728899 ERR11728857 vs ERR11728900 ERR11728857 vs ERR11728901 ERR11728857 vs ERR11728902 ERR11728857 vs ERR11728903 ERR11728857 vs ERR11728904 ERR11728857 vs ERR11728906 ERR11728857 vs ERR11728908 ERR11728857 vs ERR11728909 ERR11728857 vs ERR11728911 ERR11728857 vs ERR11728916 ERR11728857 vs ERR11728917 ERR11728857 vs ERR11728919 ERR11728857 vs ERR11728920 ERR11728857 vs ERR11728922 ERR11728857 vs ERR11728923 ERR11728857 vs ERR11728924 ERR11728857 vs ERR11728925 ERR11728857 vs ERR11728948 ERR11728857 vs ERR11728982 ERR11728857 vs ERR11728867 ERR11728857 vs ERR11728888 ERR11728857 vs ERR11728892 ERR11728857 vs ERR11728905 ERR11728857 vs ERR11728910 ERR11728857 vs ERR11728912 ERR11728857 vs ERR11728913 ERR11728857 vs ERR11728918 ERR11728857 vs ERR11728926 ERR11728857 vs ERR11728927 ERR11728857 vs ERR11728928 ERR11728857 vs ERR11728930 ERR11728857 vs ERR11728932 ERR11728857 vs ERR11728933 ERR11728857 vs ERR11728934 ERR11728857 vs ERR11728935 ERR11728857 vs ERR11728936 ERR11728857 vs ERR11728938 ERR11728857 vs ERR11728940 ERR11728857 vs ERR11728942 ERR11728857 vs ERR11728943 ERR11728857 vs ERR11728945 ERR11728857 vs ERR11728946 ERR11728857 vs ERR11728949 ERR11728857 vs ERR11728951 ERR11728857 vs ERR11728952 ERR11728857 vs ERR11728953 ERR11728857 vs ERR11728954 ERR11728857 vs ERR11728955 ERR11728857 vs 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metric	value
phenotype	MSSA_vs_MRSA
case_label	case (MRSA) (MRSA)
control_label	control (MSSA) (MSSA)
samples	100
pcoa1_variance_percent	59.8507
pcoa2_variance_percent	17.8659
pcoa1_plus_pcoa2_variance_percent	77.7166
case_within_mean_mash_distance	0.01198691088767347
control_within_mean_mash_distance	0.13918599112008162
between_group_mean_mash_distance	0.091962067764
between_within_mash_distance_ratio	1.2166
pcoa_centroid_separation_score	0.7317
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 0.73; between/within Mash distance ratio 1.22). Some GWAS signals may still be influenced by lineage, so prioritize hits that remain biologically plausible and are not explained only by clustering.
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06 Gene presence/absence GWAS plots

Brief interpretation: Gene Manhattan: Each dot is a gene or gene cluster. Taller dots mean stronger evidence of difference between the two groups. In this run, 2165 of 12794 tested gene features crossed the alpha=0.05 line. The tallest signal was group_8632 (p=3.09e-25). 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. Gene QQ: 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.
Plot note: The gene association plot is a feature-index GWAS plot, not a full reference-coordinate Manhattan plot. Significant points are interpreted against the case (MRSA) versus control (MSSA) phenotype.
Lay interpretation — gene Manhattan: Each dot is a gene or gene cluster. Taller dots mean stronger evidence of difference between the two groups. In this run, 2165 of 12794 tested gene features crossed the alpha=0.05 line. The tallest signal was group_8632 (p=3.09e-25). 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.
Lay interpretation — gene QQ: 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.
Gene presence/absence GWAS Manhattan-style association plot 24.5 19.6 14.7 9.8 4.9 0.0 alpha=0.05 Feature index -log10(p-value)
Gene presence/absence GWAS QQ plot 24.5 19.6 14.7 9.8 4.9 0.0 alpha=0.05 Expected -log10(p-value) Observed -log10(p-value) 
metric	value
pvalues_detected	12794
points_drawn	5000
plot_label	Gene presence/absence GWAS
significant_points_at_alpha	2165
top_feature	group_8632
top_pvalue	3.09e-25
top_minus_log10_pvalue	24.5100
qq_median_delta_observed_minus_expected	-0.3011
qq_tail_delta_observed_minus_expected	20.1020
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, 2165 of 12794 tested gene features crossed the alpha=0.05 line. The tallest signal was group_8632 (p=3.09e-25). 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.
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06 SNP marker GWAS

Brief interpretation: SNP Manhattan: Each dot is a SNP marker placed by reference coordinate when available. 6 of 3050 tested SNP markers crossed the alpha=0.05 line. The strongest marker was NC_007795.1_532006_A_G at position 532006 (p=0.00157). 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. SNP QQ: The SNP QQ plot does not show strong genome-wide inflation. Any outlying SNPs should still be reviewed alongside quality, recombination, and lineage information.
SNP branch: run. SNP marker GWAS is intended for mutation-mediated phenotypes, including MTBC drug-resistance traits. Review case (MRSA)/control (MSSA) population structure before interpreting SNP hits. Optional Gubbins status: not run.
Lay interpretation — SNP Manhattan: Each dot is a SNP marker placed by reference coordinate when available. 6 of 3050 tested SNP markers crossed the alpha=0.05 line. The strongest marker was NC_007795.1_532006_A_G at position 532006 (p=0.00157). 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.
Lay interpretation — SNP QQ: The SNP QQ plot does not show strong genome-wide inflation. Any outlying SNPs should still be reviewed alongside quality, recombination, and lineage information.
SNP marker GWAS Manhattan plot 2.8 2.2 1.7 1.1 0.6 0.0 alpha=0.05 Reference genomic coordinate / marker order -log10(p-value)
SNP marker GWAS QQ plot 2.8 2.2 1.7 1.1 0.6 0.0 alpha=0.05 Expected -log10(p-value) Observed -log10(p-value)

Top priority SNP marker hits

metric	value
plot_label	SNP marker GWAS
pvalues_detected	3050
significant_points_at_alpha	6
top_marker	NC_007795.1_532006_A_G
top_position	532006
top_pvalue	0.00157
top_minus_log10_pvalue	2.8041
qq_median_delta_observed_minus_expected	-0.3012
qq_tail_delta_observed_minus_expected	-0.9812
points_drawn	3050
manhattan_type	reference_coordinate_when_available
qq_plot	generated
layman_manhattan_interpretation	Each dot is a SNP marker placed by reference coordinate when available. 6 of 3050 tested SNP markers crossed the alpha=0.05 line. The strongest marker was NC_007795.1_532006_A_G at position 532006 (p=0.00157). 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 does not show strong genome-wide inflation. Any outlying SNPs should still be reviewed alongside quality, recombination, and lineage information.

SNP hit table

SNP rank 1
SAOUHSC_00529
NC_007795.1_532006_A_G | SAOUHSC_00529 | none confidence
none confidence

elongation factor G

enriched: cases (MRSA) | p=0.00157 | OR=26.1852
SNP rank 2
guaA
NC_007795.1_382630_A_G | SAOUHSC_00375 | none confidence
none confidence

GMP synthase

enriched: controls (MSSA) | p=0.0107 | OR=0.225176
SNP rank 3
rplK
NC_007795.1_518926_C_T | SAOUHSC_00518 | none confidence
none confidence

50S ribosomal protein L11

enriched: controls (MSSA) | p=0.0212 | OR=0.104084
SNP rank 4
guaA
NC_007795.1_382501_G_A | SAOUHSC_00375 | none confidence
none confidence

GMP synthase

enriched: cases (MRSA) | p=0.0226 | OR=4.10502
SNP rank 5
rpsI
NC_007795.1_2299471_G_A | SAOUHSC_02477 | none confidence
none confidence

30S ribosomal protein S9

enriched: controls (MSSA) | p=0.0297 | OR=0.0340077
rank feature id variant id feature type contig position ref alt gene name product reference locus tag reference gene reference product case (MRSA) alt case (MRSA) total case (MRSA) frequency control (MSSA) alt control (MSSA) total control (MSSA) 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_007795.1_532006_A_G NC_007795.1_532006_A_G snp NC_007795.1 532006 A G SAOUHSC_00529 elongation factor G SAOUHSC_00529 elongation factor G 10 50 0.2000 0 50 0.0000 cases (MRSA) 2.97 26.1852 1.489-460.5 1.48905 460.47 0.00157 2.8041 reference_GenBank_coordinate_overlap 531032..533113 . SNP-level association; inspect population structure before causal interpretation.
2 NC_007795.1_382630_A_G NC_007795.1_382630_A_G snp NC_007795.1 382630 A G guaA GMP synthase SAOUHSC_00375 guaA GMP synthase 2 50 0.0400 9 50 0.1800 controls (MSSA) -1.9 0.225176 0.05263-0.9634 0.0526327 0.963363 0.0107 1.9706 reference_GenBank_coordinate_overlap 381704..383245 . SNP-level association; inspect population structure before causal interpretation.
3 NC_007795.1_518926_C_T NC_007795.1_518926_C_T snp NC_007795.1 518926 C T rplK 50S ribosomal protein L11 SAOUHSC_00518 rplK 50S ribosomal protein L11 1 50 0.0200 11 50 0.2200 controls (MSSA) -1.88 0.104084 0.01805-0.6002 0.0180485 0.600245 0.0212 1.6737 reference_GenBank_coordinate_overlap 518657..519079 . SNP-level association; inspect population structure before causal interpretation.
4 NC_007795.1_382501_G_A NC_007795.1_382501_G_A snp NC_007795.1 382501 G A guaA GMP synthase SAOUHSC_00375 guaA GMP synthase 46 50 0.9200 36 50 0.7200 cases (MRSA) 1.4 4.10502 1.309-12.87 1.30891 12.8743 0.0226 1.6459 reference_GenBank_coordinate_overlap 381704..383245 . SNP-level association; inspect population structure before causal interpretation.
5 NC_007795.1_2299471_G_A NC_007795.1_2299471_G_A snp NC_007795.1 2299471 G A rpsI 30S ribosomal protein S9 SAOUHSC_02477 rpsI 30S ribosomal protein S9 0 50 0.0000 11 50 0.2200 controls (MSSA) -2.63 0.0340077 0.001944-0.595 0.00194385 0.594968 0.0297 1.5272 reference_GenBank_coordinate_overlap complement(2299327..2299725) . SNP-level association; inspect population structure before causal interpretation.
6 NC_007795.1_1197896_G_A NC_007795.1_1197896_G_A snp NC_007795.1 1197896 G A infB translation initiation factor IF-2 SAOUHSC_01246 infB translation initiation factor IF-2 1 50 0.0200 13 50 0.2600 controls (MSSA) -1.69 0.0841751 0.01478-0.4793 0.0147826 0.47931 0.0454 1.3429 reference_GenBank_coordinate_overlap 1196412..1198529 . SNP-level association; inspect population structure before causal interpretation.

Showing 6 of 6 rows.

metric	value
snp_gwas_status	prioritized
pyseer_snp_rows	3050
ranked_snp_features	3050
significant_snp_features	6
alpha	0.05
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06b Optional Gubbins recombination assessment

Brief interpretation: The recombination panel documents whether Gubbins was requested, whether filtering succeeded, and whether the SNP GWAS used the filtered or original VCF.
Recommendation: Gubbins is optional and is most useful for recombining bacterial species or datasets where recombinant blocks may inflate SNP associations. It is especially relevant for organisms such as Klebsiella pneumoniae, Escherichia coli, Salmonella, Streptococcus pneumoniae, Neisseria spp., and selected Acinetobacter datasets. For MTBC and other highly clonal organisms, keep it off by default unless there is a specific recombination or lineage-confounding question.
Requested
not requested
Run status
not run
Input SNP records
0
Filtered SNP records
0
Filtering note: Gubbins not run. When Gubbins is enabled and succeeds, SNP GWAS uses the Gubbins-filtered VCF. When it is skipped, unavailable, or fails softly, the original Snippy SNP VCF is used and the reason is recorded below.

Recombination intervals: 0. Output files: rMAP_GWAS_SNP_gubbins_summary.tsv, rMAP_GWAS_SNP_gubbins.filtered_polymorphic_sites.fasta, rMAP_GWAS_SNP_gubbins.recombination_predictions.gff, and rMAP_GWAS_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.
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07 Top priority gene presence/absence GWAS hits

Brief interpretation: The prioritized table ranks candidate gene presence/absence associations by statistical evidence, enrichment direction, effect size, and annotation support.
Rank 1
group_8632
group_8632 | SAOUHSC_00003 | none confidence | identity=42.51% | coverage=4.17%
none confidence

hypothetical protein

enriched: cases (MRSA) | p=3.09e-25 | OR=10201
Rank 2
group_7349
group_7349 | SAOUHSC_00014 | none confidence | identity=40.35% | coverage=2.33%
none confidence

hypothetical protein

enriched: cases (MRSA) | p=3.09e-25 | OR=10201
Rank 3
group_6207
group_6207 | SAOUHSC_02467 | none confidence | identity=38.23% | coverage=2.15%
none confidence

alpha-acetolactate decarboxylase

enriched: cases (MRSA) | p=3.09e-25 | OR=10201
Rank 4
mecA
mecA | SAOUHSC_00844 | none confidence | identity=20.93% | coverage=0.90%
none confidence

hypothetical protein

enriched: cases (MRSA) | p=3.09e-25 | OR=10201
Rank 5
;tnp
group_1306 | SAOUHSC_01612 | none confidence | identity=37.61% | coverage=2.52%
none confidence

2-oxoisovalerate dehydrogenase, E1 componentsubunit beta

enriched: cases (MRSA) | p=1.78e-18 | OR=691.462

Prioritized hit table

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 (MRSA) present case (MRSA) total case (MRSA) frequency control (MSSA) present control (MSSA) total control (MSSA) 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_8632 gene_presence_absence group_8632 group_8632 | SAOUHSC_00003 | none confidence group_8632 hypothetical protein SAOUHSC_00003 hypothetical protein none 42.51 4.17 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=42.51; coverage=4.17 50 50 1.0000 0 50 0.0000 cases (MRSA) 8.8 10201 198.5-5.242e+05 198.519 524185 3.09e-25 40.8265 Panaroo/Bakta+GenBank nucleotide_similarity 3670..3915 matched_representative_sequence=group_8632 AAFANJ_01646;AGNJKP_00338;BBHJIH_02625;BCINDJ_00997;BGHJOB_02138;CCGLPJ_01537;CNMMKL_01926;DBPPGI_01156;DGCAMH_02713;DHHPLE_02450;DPEBLA_02738;EAMBND_00874;EBFKMK_01383;EDBMEK_01615;EFOOKO_01444;FHPENM_01251;FIIBJA_01655;FJPBEI_02140;GGEFGC_01125;GGOGND_00016;GHNMBF_01308;GNKNJO_00279;GNNCOP_02687;HBKHOP_02629;HFCIAM_02218;HFICCC_03024;HGFBEP_01443;HJFIGM_01013;HJGKNO_01151;ILJMML_01475 hypothetical protein
2 group_7349 gene_presence_absence group_7349 group_7349 | SAOUHSC_00014 | none confidence group_7349 MaoC-like domain-containing protein SAOUHSC_00014 hypothetical protein none 40.35 2.33 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=40.35; coverage=2.33 50 50 1.0000 0 50 0.0000 cases (MRSA) 8.8 10201 198.5-5.242e+05 198.519 524185 3.09e-25 40.8265 Panaroo/Bakta+GenBank nucleotide_similarity 17365..18303 matched_representative_sequence=group_7349 AAFANJ_01644;AGNJKP_00340;BBHJIH_02623;BCINDJ_00995;BGHJOB_02140;CCGLPJ_01535;CNMMKL_01928;DBPPGI_01154;DGCAMH_02711;DHHPLE_02448;DPEBLA_02736;EAMBND_00876;EBFKMK_01381;EDBMEK_01617;EFOOKO_01446;FHPENM_01249;FIIBJA_01657;FJPBEI_02138;GGEFGC_01123;GGOGND_00014;GHNMBF_01310;GNKNJO_00277;GNNCOP_02689;HBKHOP_02627;HFCIAM_02220;HFICCC_03022;HGFBEP_01445;HJFIGM_01011;HJGKNO_01153;ILJMML_01473 hypothetical protein
3 group_6207 gene_presence_absence group_6207 group_6207 | SAOUHSC_02467 | none confidence group_6207 GP-PDE domain-containing protein SAOUHSC_02467 alpha-acetolactate decarboxylase none 38.23 2.15 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=38.23; coverage=2.15 50 50 1.0000 0 50 0.0000 cases (MRSA) 8.8 10201 198.5-5.242e+05 198.519 524185 3.09e-25 40.8265 Panaroo/Bakta+GenBank nucleotide_similarity complement(2290323..2291027) matched_representative_sequence=group_6207 AAFANJ_01645;AGNJKP_00339;BBHJIH_02624;BCINDJ_00996;BGHJOB_02139;CCGLPJ_01536;CNMMKL_01927;DBPPGI_01155;DGCAMH_02712;DHHPLE_02449;DPEBLA_02737;EAMBND_00875;EBFKMK_01382;EDBMEK_01616;EFOOKO_01445;FHPENM_01250;FIIBJA_01656;FJPBEI_02139;GGEFGC_01124;GGOGND_00015;GHNMBF_01309;GNKNJO_00278;GNNCOP_02688;HBKHOP_02628;HFCIAM_02219;HFICCC_03023;HGFBEP_01444;HJFIGM_01012;HJGKNO_01152;ILJMML_01474 alpha-acetolactate decarboxylase
4 mecA gene_presence_absence mecA mecA | SAOUHSC_00844 | none confidence mecA PBP2a family beta-lactam-resistant peptidoglycan transpeptidase MecA SAOUHSC_00844 hypothetical protein none 20.93 0.90 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=20.93; coverage=0.90 50 50 1.0000 0 50 0.0000 cases (MRSA) 8.8 10201 198.5-5.242e+05 198.519 524185 3.09e-25 40.8265 Panaroo/Bakta+GenBank nucleotide_similarity 814851..815672 matched_representative_sequence=mecA AAFANJ_01643;AGNJKP_00341;BBHJIH_02622;BCINDJ_00994;BGHJOB_02141;CCGLPJ_01534;CNMMKL_01929;DBPPGI_01153;DGCAMH_02710;DHHPLE_02447;DPEBLA_02735;EAMBND_00877;EBFKMK_01380;EDBMEK_01618;EFOOKO_01447;FHPENM_01248;FIIBJA_01658;FJPBEI_02137;GGEFGC_01122;GGOGND_00013;GHNMBF_01311;GNKNJO_00276;GNNCOP_02690;HBKHOP_02626;HFCIAM_02221;HFICCC_03021;HGFBEP_01446;HJFIGM_01010;HJGKNO_01154;ILJMML_01472 hypothetical protein
5 group_1306 gene_presence_absence ;tnp group_1306 | SAOUHSC_01612 | none confidence ;tnp hypothetical protein;IS6 family IS431R transposase;IS6 family IS431mec transposase SAOUHSC_01612 2-oxoisovalerate dehydrogenase, E1 componentsubunit beta none 37.61 2.52 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=37.61; coverage=2.52 44 50 0.8800 0 50 0.0000 cases (MRSA) 6.16 691.462 37.87-1.262e+04 37.8724 12624.5 1.78e-18 30.1831 Panaroo/Bakta+GenBank nucleotide_similarity complement(1535924..1536907) matched_representative_sequence=49_refound_346 25_refound_104;49_refound_346;59_refound_385_pseudo;60_refound_389_pseudo;70_refound_452_pseudo;85_refound_544_pseudo;89_refound_567_pseudo;90_refound_571;94_refound_594_pseudo;AAFANJ_01647;AGNJKP_00337;BGHJOB_02137;CCGLPJ_01538;CNMMKL_01930;DBPPGI_01157;DHHPLE_02451;EAMBND_00873;EBFKMK_01384;EDBMEK_01614;EFOOKO_01443;FHPENM_01252;FIIBJA_01654;FJPBEI_02141;GGEFGC_01126;GGOGND_00017;GHNMBF_01307;GNKNJO_00280;GNNCOP_02691;HFCIAM_02217;HFICCC_04308 2-oxoisovalerate dehydrogenase, E1 componentsubunit beta
6 group_5731 gene_presence_absence group_5731 group_5731 | SAOUHSC_00469 | none confidence group_5731 hypothetical protein;Phage protein SAOUHSC_00469 regulatory protein SpoVG none 34.34 16.13 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=34.34; coverage=16.13 46 50 0.9200 5 50 0.1000 cases (MRSA) 6.21 85.4848 23.04-317.2 23.0382 317.198 1.5e-19 28.2415 Panaroo/Bakta+GenBank nucleotide_similarity 468929..469231 matched_representative_sequence=group_5731 AAFANJ_01637;AGNJKP_00347;BBHJIH_02611;BCINDJ_00988;BGHJOB_02147;CCGLPJ_01523;CJHDKP_02388;CLDKNN_00890;DBPPGI_01147;DGCAMH_02699;DHHPLE_02436;DPEBLA_02459;EAMBND_02662;EBFKMK_01369;EDBMEK_01624;EFOOKO_01453;FFPFOI_02215;FHPENM_01242;FIIBJA_01664;FJPBEI_02126;FMNEAL_02262;GGEFGC_01116;GGOGND_00007;GHNMBF_01317;GNKNJO_00270;GNNCOP_02700;HBKHOP_02615;HFCIAM_02227;HFICCC_03015;HGFBEP_01452 regulatory protein SpoVG
7 group_5706 gene_presence_absence group_5706 group_5706 | SAOUHSC_00753 | none confidence group_5706 Pyridoxal phosphate-dependent enzyme;hypothetical protein SAOUHSC_00753 hypothetical protein none 22.38 5.13 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=22.38; coverage=5.13 46 50 0.9200 5 50 0.1000 cases (MRSA) 6.21 85.4848 23.04-317.2 23.0382 317.198 1.5e-19 28.2415 Panaroo/Bakta+GenBank nucleotide_similarity complement(736562..737080) matched_representative_sequence=group_5706 AAFANJ_01638;AGNJKP_00346;BBHJIH_02610;BCINDJ_00989;BGHJOB_02146;CCGLPJ_01522;CJHDKP_02389;CLDKNN_00891;DBPPGI_01148;DGCAMH_02698;DHHPLE_02435;DPEBLA_02460;EAMBND_02661;EBFKMK_01368;EDBMEK_01623;EFOOKO_01452;FFPFOI_02216;FHPENM_01243;FIIBJA_01663;FJPBEI_02125;FMNEAL_02261;GGEFGC_01117;GGOGND_00008;GHNMBF_01316;GNKNJO_00271;GNNCOP_02701;HBKHOP_02614;HFCIAM_02226;HFICCC_03016;HGFBEP_01451 hypothetical protein
8 group_5704 gene_presence_absence group_5704 group_5704 | SAOUHSC_00027 | none confidence group_5704 Transposase;DUF1643 domain-containing protein SAOUHSC_00027 23S rRNA(pseudouridine(1915)-N(3))-methyltransferase RlmH none 42.35 1.78 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=42.35; coverage=1.78 46 50 0.9200 5 50 0.1000 cases (MRSA) 6.21 85.4848 23.04-317.2 23.0382 317.198 1.5e-19 28.2415 Panaroo/Bakta+GenBank nucleotide_similarity 33691..34170 matched_representative_sequence=group_5704 AAFANJ_01639;AGNJKP_00345;BBHJIH_02609;BCINDJ_00990;BGHJOB_02145;CCGLPJ_01521;CJHDKP_02390;CLDKNN_00892;DBPPGI_01149;DGCAMH_02697;DHHPLE_02434;DPEBLA_02461;EAMBND_02660;EBFKMK_01367;EDBMEK_01622;EFOOKO_01451;FFPFOI_02217;FHPENM_01244;FIIBJA_01662;FJPBEI_02124;FMNEAL_02260;GGEFGC_01118;GGOGND_00009;GHNMBF_01315;GNKNJO_00272;GNNCOP_02702;HBKHOP_02613;HFCIAM_02225;HFICCC_03017;HGFBEP_01450 23S rRNA(pseudouridine(1915)-N(3))-methyltransferase RlmH
9 group_4661 gene_presence_absence group_4661 group_4661 | SAOUHSC_03000 | none confidence group_4661 hypothetical protein;Transposon tn552 dna-invertase binr SAOUHSC_03000 capsular polysaccharide biosynthesis proteinCapA none 20.59 0.98 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=20.59; coverage=0.98 31 50 0.6200 0 50 0.0000 cases (MRSA) 6.05 163.154 9.511-2799 9.5112 2798.72 1.51e-12 22.1711 Panaroo/Bakta+GenBank nucleotide_similarity complement(2772939..2773601) matched_representative_sequence=group_4661 AAFANJ_01635;AGNJKP_00349;BCINDJ_00986;BGHJOB_02149;DBPPGI_01145;DPEBLA_02456;DPEBLA_02457;EAMBND_02664;EDBMEK_01626;EFOOKO_01455;FHPENM_01240;FIIBJA_01666;GGEFGC_01114;GGOGND_00005;GHNMBF_01319;GNKNJO_00268;HFCIAM_02229;HFICCC_03013;HGFBEP_01454;HJFIGM_01002;HJGKNO_01162;ILJMML_01464;KOFDAJ_02645;NBILEO_02656;NCJOOM_00377;NJAOBP_03670;NKBKLH_01902;NMHDHA_01202;PBDKDP_00805;PHCLFM_01334 capsular polysaccharide biosynthesis proteinCapA
10 group_4071 gene_presence_absence group_4071 group_4071 | SAOUHSC_01015 | none confidence group_4071 DUF927 domain-containing protein SAOUHSC_01015 phosphoribosylaminoimidazole synthetase none 21.40 0.89 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=21.40; coverage=0.89 31 50 0.6200 0 50 0.0000 cases (MRSA) 6.05 163.154 9.511-2799 9.5112 2798.72 1.51e-12 22.1711 Panaroo/Bakta+GenBank nucleotide_similarity 986197..987225 matched_representative_sequence=group_4071 AAFANJ_01633;AGNJKP_00351;BCINDJ_00984;BGHJOB_02151;DBPPGI_01143;DPEBLA_02454;EAMBND_02667;EDBMEK_01628;EFOOKO_01457;FHPENM_01238;FIIBJA_01668;GGEFGC_01112;GGOGND_00003;GHNMBF_01321;GNKNJO_00266;HFCIAM_02231;HFICCC_03011;HGFBEP_01456;HJFIGM_01000;HJGKNO_01164;ILJMML_01462;KOFDAJ_02643;NBILEO_02654;NCJOOM_00375;NJAOBP_03668;NKBKLH_01900;NMHDHA_01200;PBDKDP_00803;PHCLFM_01336;PKCIIG_00851 phosphoribosylaminoimidazole synthetase
11 mecR1 gene_presence_absence mecR1 mecR1 | SAOUHSC_00005 | none confidence mecR1 beta-lactam sensor/signal transducer MecR1 SAOUHSC_00005 DNA gyrase subunit B none 34.09 1.11 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=34.09; coverage=1.11 31 50 0.6200 0 50 0.0000 cases (MRSA) 6.05 163.154 9.511-2799 9.5112 2798.72 1.62e-12 22.1406 Panaroo/Bakta+GenBank nucleotide_similarity 5034..6968 matched_representative_sequence=mecR1 AAFANJ_01642;AGNJKP_00342;BCINDJ_00993;BGHJOB_02142;DBPPGI_01152;EAMBND_00878;EDBMEK_01619;EFOOKO_01448;FHPENM_01247;FIIBJA_01659;GGEFGC_01121;GGOGND_00012;GHNMBF_01312;GNKNJO_00275;HFCIAM_02222;HFICCC_03020;HGFBEP_01447;HJFIGM_01009;HJGKNO_01155;ILJMML_01471;KOFDAJ_01933;MGNIJD_00584;NBILEO_01984;NCJOOM_00384;NJAOBP_03677;NKBKLH_01909;NMHDHA_01209;PBDKDP_00812;PHCLFM_01327;PKCIIG_00861 DNA gyrase subunit B
12 group_5724 gene_presence_absence group_5724 group_5724 | SAOUHSC_02801 | none confidence group_5724 UTP-glucose-1-phosphate uridylyltransferase SAOUHSC_02801 UTP-glucose-1-phosphate uridylyltransferase none 33.43 1.27 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=33.43; coverage=1.27 29 50 0.5800 0 50 0.0000 cases (MRSA) 6.16 138.581 8.093-2373 8.09304 2373 7.52e-12 21.2384 Panaroo/Bakta+GenBank nucleotide_similarity complement(2576833..2577615) matched_representative_sequence=group_5724 AAFANJ_01649;AGNJKP_00335;BGHJOB_02136;DBPPGI_01159;DPEBLA_02444;EAMBND_00870;EAMBND_00871;EDBMEK_01612;EFOOKO_01441;FHPENM_01254;FIIBJA_01652;GGEFGC_01128;GGOGND_00019;GHNMBF_01305;GNKNJO_00282;GNKNJO_00283;HFCIAM_02215;HFICCC_04118;HGFBEP_01437;HJGKNO_01148;ILJMML_01478;KOFDAJ_01925;KOFDAJ_01926;MGNIJD_01845;NBILEO_01976;NBILEO_01977;NCJOOM_00391;NCJOOM_00392;NJAOBP_05133;NKBKLH_01915 UTP-glucose-1-phosphate uridylyltransferase
13 group_4347 gene_presence_absence recA; group_4347 | SAOUHSC_01716 | none confidence recA; Recombinase RecA;hypothetical protein SAOUHSC_01716 hypothetical protein none 19.09 1.11 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=19.09; coverage=1.11 27 50 0.5400 0 50 0.0000 cases (MRSA) 5.81 118.191 6.909-2022 6.90926 2021.81 7.89e-11 19.9879 Panaroo/Bakta+GenBank nucleotide_similarity complement(1621052..1622320) matched_representative_sequence=group_4347 AAFANJ_01634;AGNJKP_00350;BGHJOB_02150;DBPPGI_01144;DPEBLA_02455;EAMBND_02665;EAMBND_02666;EDBMEK_01627;EFOOKO_01456;FHPENM_01239;FIIBJA_01667;GGEFGC_01113;GGOGND_00004;GHNMBF_01320;GNKNJO_00267;HFCIAM_02230;HFICCC_03012;HGFBEP_01455;HJGKNO_01163;ILJMML_01463;KOFDAJ_02644;NBILEO_02655;NJAOBP_03669;NKBKLH_01901;NMHDHA_01201;PHCLFM_01335;PKCIIG_00852;PKFOMJ_01317 hypothetical protein
14 group_5720 gene_presence_absence rplI group_5720 | SAOUHSC_00017 | none confidence rplI hypothetical protein;Type I restriction-modification system restriction subunit R SAOUHSC_00017 rplI 50S ribosomal protein L9 none 35.01 3.45 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=35.01; coverage=3.45 31 50 0.6200 2 50 0.0400 cases (MRSA) 6.05 31.3385 7.798-125.9 7.79804 125.942 1.55e-12 19.7795 Panaroo/Bakta+GenBank nucleotide_similarity 20282..20734 matched_representative_sequence=group_5720 AAFANJ_01641;AGNJKP_00343;BCINDJ_00992;BGHJOB_02143;CPFPLH_01651;CPMMBP_01651;DBPPGI_01151;EAMBND_00879;EDBMEK_01620;EFOOKO_01449;FHPENM_01246;FIIBJA_01660;GGEFGC_01120;GGOGND_00011;GHNMBF_01313;GNKNJO_00274;HFCIAM_02223;HFICCC_03019;HGFBEP_01448;HJFIGM_01008;HJGKNO_01156;ILJMML_01470;KOFDAJ_01934;MGNIJD_00585;NBILEO_01985;NCJOOM_00383;NJAOBP_03676;NKBKLH_01908;NMHDHA_01208;PBDKDP_00811 50S ribosomal protein L9
15 group_5764 gene_presence_absence group_5764 group_5764 | SAOUHSC_01154 | none confidence group_5764 hypothetical protein SAOUHSC_01154 hypothetical protein none 38.47 4.27 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=38.47; coverage=4.27 32 50 0.6400 5 50 0.1000 cases (MRSA) 6.42 14.5332 5.071-41.65 5.07059 41.6546 4.46e-13 19.2119 Panaroo/Bakta+GenBank nucleotide_similarity 1104514..1105077 matched_representative_sequence=group_5764 AAFANJ_01636;AGNJKP_00348;BCINDJ_00987;BGHJOB_02148;CJHDKP_02387;CLDKNN_00889;DBPPGI_01146;DPEBLA_02458;EAMBND_02663;EDBMEK_01625;EFOOKO_01454;FFPFOI_02214;FHPENM_01241;FIIBJA_01665;FMNEAL_02263;GGEFGC_01115;GGOGND_00006;GHNMBF_01318;GNKNJO_00269;HFCIAM_02228;HFICCC_03014;HGFBEP_01453;HJFIGM_01003;HJGKNO_01161;ILJMML_01465;JFACDE_02170;KOFDAJ_02646;MGNIJD_00590;NBILEO_02657;NCJOOM_00378 hypothetical protein
16 group_8214 gene_presence_absence group_8214 group_8214 | SAOUHSC_02176 | none confidence group_8214 hypothetical protein SAOUHSC_02176 hypothetical protein none 38.37 6.25 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=38.37; coverage=6.25 25 50 0.5000 0 50 0.0000 cases (MRSA) 5.4 101 5.906-1727 5.90622 1727.16 9e-10 18.7040 Panaroo/Bakta+GenBank nucleotide_similarity complement(2037590..2037766) matched_representative_sequence=group_8214 AAFANJ_01648;AGNJKP_00336;DBPPGI_01158;EAMBND_00872;EDBMEK_01613;EFOOKO_01442;FHPENM_01253;FIIBJA_01653;GGEFGC_01127;GGOGND_00018;GHNMBF_01306;GNKNJO_00281;HFCIAM_02216;HFICCC_04119;HGFBEP_01441;HJGKNO_01149;ILJMML_01477;KOFDAJ_01927;MGNIJD_01846;NBILEO_01978;NCJOOM_00390;NJAOBP_05134;NMHDHA_01215;PHCLFM_01321;PKFOMJ_01331 hypothetical protein
17 group_8016 gene_presence_absence group_8016 group_8016 | SAOUHSC_00037 | none confidence group_8016 hypothetical protein SAOUHSC_00037 hypothetical protein none 19.93 5.15 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=19.93; coverage=5.15 23 50 0.4600 0 50 0.0000 cases (MRSA) 5.24 86.3091 5.045-1476 5.04547 1476.42 4.78e-09 17.7520 Panaroo/Bakta+GenBank nucleotide_similarity 40821..42014 matched_representative_sequence=group_8016 AAFANJ_01632;BGHJOB_02152;DBPPGI_01142;EAMBND_02668;EDBMEK_01629;EFOOKO_01458;FHPENM_01237;FIIBJA_01669;GGEFGC_01111;GGOGND_00002;GHNMBF_01322;GNKNJO_00265;HFCIAM_02232;HFICCC_03010;HJGKNO_01165;ILJMML_01461;KOFDAJ_02642;NBILEO_02653;NJAOBP_03667;NKBKLH_01899;NMHDHA_01199;PHCLFM_01337;PKFOMJ_01315 hypothetical protein
18 group_7603 gene_presence_absence rplP group_7603 | SAOUHSC_02505 | none confidence rplP 5-methylcytosine-specific restriction enzyme a SAOUHSC_02505 rplP 50S ribosomal protein L16 none 37.92 4.57 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=37.92; coverage=4.57 23 50 0.4600 0 50 0.0000 cases (MRSA) 5.24 86.3091 5.045-1476 5.04547 1476.42 4.78e-09 17.7520 Panaroo/Bakta+GenBank nucleotide_similarity complement(2313509..2313943) matched_representative_sequence=group_7603 AAFANJ_01628;BGHJOB_01267;DBPPGI_00788;EAMBND_02491;EDBMEK_00450;EFOOKO_00476;FHPENM_00913;FIIBJA_00989;GGEFGC_02528;GGOGND_02602;GHNMBF_02580;GNKNJO_02552;HFCIAM_01255;HFICCC_03006;HJGKNO_00519;ILJMML_00862;KOFDAJ_02546;NBILEO_02571;NJAOBP_04407;NKBKLH_01240;NMHDHA_02596;PHCLFM_00408;PKFOMJ_01311 50S ribosomal protein L16
19 group_6616 gene_presence_absence group_6616 group_6616 | SAOUHSC_00942 | none confidence group_6616 Restriction endonuclease SAOUHSC_00942 GTP pyrophosphokinase none 43.75 2.58 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=43.75; coverage=2.58 23 50 0.4600 0 50 0.0000 cases (MRSA) 5.24 86.3091 5.045-1476 5.04547 1476.42 4.78e-09 17.7520 Panaroo/Bakta+GenBank nucleotide_similarity 914181..914816 matched_representative_sequence=group_6616 AAFANJ_01627;BGHJOB_01268;DBPPGI_00787;EAMBND_02492;EDBMEK_00451;EFOOKO_00477;FHPENM_00912;FIIBJA_00990;GGEFGC_02527;GGOGND_02601;GHNMBF_02581;GNKNJO_02551;HFCIAM_01256;HFICCC_03005;HJGKNO_00520;ILJMML_00861;KOFDAJ_02545;NBILEO_02570;NJAOBP_04406;NKBKLH_01239;NMHDHA_02595;PHCLFM_00409;PKFOMJ_01310 GTP pyrophosphokinase
20 group_2737 gene_presence_absence group_2737 group_2737 | SAOUHSC_00036 | none confidence group_2737 Metallo-beta-lactamase domain-containing protein SAOUHSC_00036 hypothetical protein none 63.08 2.09 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=63.08; coverage=2.09 23 50 0.4600 0 50 0.0000 cases (MRSA) 5.24 86.3091 5.045-1476 5.04547 1476.42 4.78e-09 17.7520 Panaroo/Bakta+GenBank nucleotide_similarity 39468..40802 matched_representative_sequence=group_2737 AAFANJ_01629;BGHJOB_01266;DBPPGI_00789;EAMBND_02490;EDBMEK_00449;EFOOKO_00475;FHPENM_00914;FIIBJA_00988;GGEFGC_02529;GGOGND_02603;GHNMBF_02579;GNKNJO_02553;HFCIAM_01254;HFICCC_03007;HJGKNO_00518;ILJMML_00863;KOFDAJ_02547;NBILEO_02572;NJAOBP_04409;NKBKLH_01241;NMHDHA_02597;PHCLFM_00407;PKFOMJ_01312 hypothetical protein
21 group_2330 gene_presence_absence group_2330 group_2330 | SAOUHSC_00932 | none confidence group_2330 ACP synthase SAOUHSC_00932 oligopeptide ABC transporter permease none 30.23 1.52 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=30.23; coverage=1.52 23 50 0.4600 0 50 0.0000 cases (MRSA) 5.24 86.3091 5.045-1476 5.04547 1476.42 4.78e-09 17.7520 Panaroo/Bakta+GenBank nucleotide_similarity 904625..905506 matched_representative_sequence=group_2330 AAFANJ_01631;BGHJOB_02153;DBPPGI_01141;EAMBND_02669;EDBMEK_01630;EFOOKO_01459;FHPENM_01236;FIIBJA_01670;GGEFGC_01110;GGOGND_00001;GHNMBF_01323;GNKNJO_00264;HFCIAM_02233;HFICCC_03009;HJGKNO_01166;ILJMML_01460;KOFDAJ_02641;NBILEO_02652;NJAOBP_03666;NKBKLH_01898;NMHDHA_01198;PHCLFM_01338;PKFOMJ_01314 oligopeptide ABC transporter permease
22 group_470 gene_presence_absence group_470 group_470 | SAOUHSC_02667 | none confidence group_470 Transcriptional regulator SAOUHSC_02667 hypothetical protein none 91.39 6.26 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=91.39; coverage=6.26 23 50 0.4600 0 50 0.0000 cases (MRSA) 5.24 86.3091 5.045-1476 5.04547 1476.42 4.78e-09 17.7520 Panaroo/Bakta+GenBank nucleotide_similarity complement(2452049..2453326) matched_representative_sequence=group_4707 AAFANJ_01630;BGHJOB_01265;DBPPGI_00790;EAMBND_02489;EDBMEK_00448;EFOOKO_00474;FHPENM_00915;FIIBJA_00987;GGEFGC_02530;GGOGND_02604;GHNMBF_02578;GNKNJO_02554;HFCIAM_01253;HFICCC_03008;HJGKNO_00517;ILJMML_00864;KOFDAJ_02548;NBILEO_02573;NJAOBP_04410;NKBKLH_01242;NMHDHA_02598;PHCLFM_00406;PKFOMJ_01313 hypothetical protein
23 fusC gene_presence_absence fusC fusC | SAOUHSC_00881 | none confidence fusC fusidic acid resistance EF-G-binding protein FusC SAOUHSC_00881 hypothetical protein none 35.50 2.50 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=35.50; coverage=2.50 25 50 0.5000 0 50 0.0000 cases (MRSA) 4.37 101 5.906-1727 5.90622 1727.16 2.98e-08 17.1840 Panaroo/Bakta+GenBank nucleotide_similarity 846360..846734 matched_representative_sequence=fusC AAFANJ_01671;BBHJIH_02392;BCINDJ_00977;CCGLPJ_01142;CNMMKL_01942;DGCAMH_01205;DHHPLE_02430;DPEBLA_02448;EBFKMK_01363;FIIBJA_01630;HBKHOP_02435;HJFIGM_00994;JHLLHD_02319;JPKDEA_02390;KBDKBJ_02551;LPHLDL_02437;NCJOOM_00369;NNICCC_00250;NPGDHH_01376;OAHHLH_06628;OMNKFL_02464;PBDKDP_00797;PJCLAL_01208;PKCIIG_00845;PKFOMJ_01354 hypothetical protein
24 group_908 gene_presence_absence group_908 group_908 | SAOUHSC_01228 | none confidence group_908 DUF771 domain-containing protein;hypothetical protein SAOUHSC_01228 transcriptional repressor CodY none 65.63 4.26 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=65.63; coverage=4.26 25 50 0.5000 0 50 0.0000 cases (MRSA) 4.37 101 5.906-1727 5.90622 1727.16 2.98e-08 17.1840 Panaroo/Bakta+GenBank nucleotide_similarity 1179705..1180478 matched_representative_sequence=group_9085 AAFANJ_01672;BBHJIH_02391;BCINDJ_00978;CCGLPJ_01141;CNMMKL_01943;DGCAMH_01206;DHHPLE_02431;DPEBLA_02449;EBFKMK_01364;FIIBJA_01629;HBKHOP_02436;HJFIGM_00995;JHLLHD_02320;JPKDEA_02389;KBDKBJ_02550;LPHLDL_02438;NCJOOM_00370;NNICCC_00249;NPGDHH_01375;OAHHLH_06627;OMNKFL_02463;PBDKDP_00798;PJCLAL_01207;PKCIIG_00846;PKFOMJ_01355 transcriptional repressor CodY
25 group_1790 gene_presence_absence yoeB; group_1790 | SAOUHSC_02756 | none confidence yoeB; Putative mRNA interferase YoeB;Txe/YoeB family addiction module toxin SAOUHSC_02756 hypothetical protein none 95.51 18.35 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=95.51; coverage=18.35 46 50 0.9200 13 50 0.2600 cases (MRSA) 3.09 28.7037 9.085-90.68 9.08545 90.6837 3.2e-08 15.3380 Panaroo/Bakta+GenBank nucleotide_similarity complement(2534034..2534300) matched_representative_sequence=group_1790 AAFANJ_01964;AGNJKP_00048;BBHJIH_01486;BCINDJ_01652;BGHJOB_01913;CCGLPJ_01988;CKFMFB_00238;CNMMKL_00582;DBPPGI_01705;DGCAMH_01518;DHHPLE_01484;DPEBLA_01700;EAMBND_01061;EBFKMK_01627;EBHIAF_01777;EDBMEK_01868;EEPHOB_01301;EFOOKO_01973;EOFOFH_01680;FHPENM_02417;FIIBJA_01713;FJPBEI_01205;FMOEEE_01426;GGEFGC_01674;GGOGND_00304;GHNMBF_01989;GNFCHG_01431;GNKNJO_01007;GNNCOP_01677;HBKHOP_01496 hypothetical protein
26 group_5705 gene_presence_absence group_5705 group_5705 | SAOUHSC_01005 | none confidence group_5705 ISSau3 transposase;Transposase SAOUHSC_01005 hypothetical protein none 19.76 0.92 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=19.76; coverage=0.92 28 50 0.5600 2 50 0.0400 cases (MRSA) 3.48 24.5733 6.144-98.28 6.14429 98.278 3.04e-08 15.1361 Panaroo/Bakta+GenBank nucleotide_similarity complement(977138..977455) matched_representative_sequence=group_5705 AAFANJ_01640;AGNJKP_00344;BCINDJ_00991;BGHJOB_02144;DBPPGI_01150;EDBMEK_01621;EFOOKO_01450;FHPENM_01245;FIIBJA_01661;GGEFGC_01119;GGOGND_00010;GHNMBF_01314;GNKNJO_00273;HFCIAM_02224;HFICCC_03018;HGAGGM_00189;HGFBEP_01449;HJFIGM_01007;HJGKNO_01157;IGAMFP_01293;ILJMML_01469;MGNIJD_00586;NCJOOM_00382;NJAOBP_03675;NKBKLH_01907;NMHDHA_01207;PBDKDP_00810;PHCLFM_01329;PKCIIG_00858;PKFOMJ_01323 hypothetical protein
27 group_3186 gene_presence_absence dnaD; group_3186 | SAOUHSC_00017 | none confidence dnaD; DnaD domain-containing protein;hypothetical protein;DnaD domain protein SAOUHSC_00017 rplI 50S ribosomal protein L9 none 35.34 1.01 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=35.34; coverage=1.01 39 50 0.7800 7 50 0.1400 cases (MRSA) 2.76 19.9217 7.214-55.01 7.21397 55.0149 2.08e-08 14.9982 Panaroo/Bakta+GenBank nucleotide_similarity 20282..20734 matched_representative_sequence=group_3186 AAFANJ_02595;AGNJKP_02359;BBHJIH_02146;BGHJOB_02221;CNMMKL_00105;DBPPGI_02327;DHHPLE_02143;DPEBLA_01889;EAMBND_02602;EDBMEK_02516;EFOOKO_02384;FCNEHE_02085;FHJCBG_02287;FHPENM_01777;FIIBJA_02041;FMOEEE_00552;GGEFGC_02297;GGOGND_02255;GHNMBF_02177;GNKNJO_02639;HBKHOP_02220;HFCIAM_02358;HFICCC_03938;HGAGGM_02617;HJGKNO_02404;HLEGMA_02333;IGAMFP_02126;ILJMML_02513;JHLLHD_02072;JPKDEA_02103 50S ribosomal protein L9
28 group_5259 gene_presence_absence group_5259 group_5259 | SAOUHSC_00404 | none confidence group_5259 Uncharacterized lipoprotein SA0399;Uncharacterized lipoprotein SAB0394;Uncharacterized lipoprotein SAOUHSC_00404;Csa1 family protein;hypothetical protein SAOUHSC_00404 hypothetical protein none 63.66 6.27 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=63.66; coverage=6.27 37 50 0.7400 7 50 0.1400 cases (MRSA) 3.13 16.1111 5.964-43.52 5.96413 43.5215 6.56e-08 14.1931 Panaroo/Bakta+GenBank nucleotide_similarity 406302..407087 matched_representative_sequence=group_5259 AAFANJ_01291;BBHJIH_02505;BCINDJ_02669;CNMMKL_02113;DBPPGI_00444;DHHPLE_02539;EAMBND_01305;EBHIAF_02542;EDBMEK_00794;EEPHOB_02302;EEPHOB_02303;EFOOKO_00820;FCNEHE_01319;FHPENM_00568;FIIBJA_01327;FJPBEI_01017;FMOEEE_02003;GGEFGC_00444;GGOGND_00831;GHNMBF_00489;GNKNJO_01069;GNNCOP_00040;HBKHOP_02508;HFCIAM_01594;HFICCC_04060;HGAGGM_01666;HGFBEP_02075;HJFIGM_02553;HJGKNO_00864;HLEGMA_01304 hypothetical protein
29 group_7350 gene_presence_absence group_7350 group_7350 | SAOUHSC_02564 | none confidence group_7350 Glyoxalase/fosfomycin resistance/dioxygenase domain-containing protein SAOUHSC_02564 urease accessory protein UreG none 36.21 3.73 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=36.21; coverage=3.73 19 50 0.3800 0 50 0.0000 cases (MRSA) 3.73 62.5238 3.645-1073 3.64488 1072.52 6.88e-06 14.1287 Panaroo/Bakta+GenBank nucleotide_similarity 2355860..2356474 matched_representative_sequence=group_7350 BBHJIH_02620;CCGLPJ_01532;CNMMKL_01924;DGCAMH_02708;DHHPLE_02445;DPEBLA_02746;EBFKMK_01378;FJPBEI_02135;GNNCOP_02692;HBKHOP_02624;JHLLHD_02651;JPKDEA_02622;KBDKBJ_02756;LPHLDL_02452;NNICCC_00267;NPGDHH_02733;OAHHLH_06612;OMNKFL_02691;PJCLAL_02764 urease accessory protein UreG
30 group_3788 gene_presence_absence group_3788 group_3788 | SAOUHSC_00598 | none confidence group_3788 Transcriptional regulator SAOUHSC_00598 hypothetical protein none 28.00 1.72 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=28.00; coverage=1.72 19 50 0.3800 0 50 0.0000 cases (MRSA) 3.73 62.5238 3.645-1073 3.64488 1072.52 6.88e-06 14.1287 Panaroo/Bakta+GenBank nucleotide_similarity 593183..593752 matched_representative_sequence=group_3788 BBHJIH_02619;CCGLPJ_01531;CNMMKL_01923;DGCAMH_02707;DHHPLE_02444;DPEBLA_02747;EBFKMK_01377;FJPBEI_02134;GNNCOP_02693;HBKHOP_02623;JHLLHD_02650;JPKDEA_02621;KBDKBJ_02755;LPHLDL_02451;NNICCC_00268;NPGDHH_02732;OAHHLH_06613;OMNKFL_02690;PJCLAL_02763 hypothetical protein
31 spn gene_presence_absence SAOUHSC_00401-like (spn) spn | SAOUHSC_00401 | low confidence spn myeloperoxidase inhibitor SPIN SAOUHSC_00401 hypothetical protein low 99.35 49.19 Low-confidence locus-level GenBank rescue. identity=99.35; coverage=49.19 50 50 1.0000 29 50 0.5800 cases (MRSA) 37.1 73.6102 4.299-1260 4.29877 1260.47 2.13e-05 13.8735 Panaroo/Bakta+GenBank nucleotide_similarity complement(404819..405127) matched_representative_sequence=25_refound_103 0_refound_3;25_refound_103;30_refound_135;46_refound_294;56_refound_368;57_refound_378;61_refound_395;65_refound_430;67_refound_440;69_refound_446;72_refound_462;78_refound_506;79_refound_511;83_refound_527;91_refound_573;93_refound_586;96_refound_605;98_refound_617;99_refound_621;AGNJKP_00699;BBHJIH_02502;BCINDJ_02666;BGHJOB_02675;BLNHMO_01869;CCGLPJ_01482;CDDCHJ_01623;CIALCM_01878;CJJPLC_01922;CKFMFB_02200;DGCAMH_00865 hypothetical protein
32 group_7923 gene_presence_absence groES group_7923 | SAOUHSC_02255 | none confidence groES Pyridoxal phosphate-dependent enzyme SAOUHSC_02255 groES co-chaperonin GroES none 33.50 4.81 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=33.50; coverage=4.81 18 50 0.3600 0 50 0.0000 cases (MRSA) 3.63 57.4923 3.348-987.4 3.3475 987.412 1.48e-05 13.6750 Panaroo/Bakta+GenBank nucleotide_similarity complement(2088452..2088736) matched_representative_sequence=group_7923 BBHJIH_02592;CCGLPJ_01540;CNMMKL_01932;DGCAMH_01210;DHHPLE_02453;DPEBLA_01173;EBFKMK_01386;GNNCOP_01027;HBKHOP_02595;JHLLHD_02602;JPKDEA_02608;KBDKBJ_02559;LPHLDL_02460;NNICCC_00259;NPGDHH_01385;OAHHLH_06604;OMNKFL_02678;PJCLAL_02185 co-chaperonin GroES
33 group_7771 gene_presence_absence group_7771 group_7771 | SAOUHSC_02331 | none confidence group_7771 Phage protein SAOUHSC_02331 hypothetical protein none 7.58 4.42 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=7.58; coverage=4.42 18 50 0.3600 0 50 0.0000 cases (MRSA) 3.63 57.4923 3.348-987.4 3.3475 987.412 1.48e-05 13.6750 Panaroo/Bakta+GenBank nucleotide_similarity complement(2161547..2162236) matched_representative_sequence=group_7771 BBHJIH_02593;CCGLPJ_01541;CNMMKL_01934;DGCAMH_01211;DHHPLE_02454;DPEBLA_01172;EBFKMK_01387;GNNCOP_01026;HBKHOP_02596;JHLLHD_02603;JPKDEA_02607;KBDKBJ_02558;LPHLDL_02461;NNICCC_00258;NPGDHH_01383;OAHHLH_06602;OMNKFL_02677;PJCLAL_02184 hypothetical protein
34 group_7016 gene_presence_absence group_7016 group_7016 | SAOUHSC_01949 | none confidence group_7016 Transposase SAOUHSC_01949 intracellular serine protease none 25.52 3.16 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=25.52; coverage=3.16 18 50 0.3600 0 50 0.0000 cases (MRSA) 3.63 57.4923 3.348-987.4 3.3475 987.412 1.48e-05 13.6750 Panaroo/Bakta+GenBank nucleotide_similarity complement(1851533..1852906) matched_representative_sequence=group_7016 BBHJIH_02591;CCGLPJ_01539;CNMMKL_01931;DGCAMH_01209;DHHPLE_02452;DPEBLA_01174;EBFKMK_01385;GNNCOP_01028;HBKHOP_02594;JHLLHD_02601;JPKDEA_02609;KBDKBJ_02560;LPHLDL_02459;NNICCC_00260;NPGDHH_01386;OAHHLH_06605;OMNKFL_02679;PJCLAL_02186 intracellular serine protease
35 group_5287 gene_presence_absence group_5287 group_5287 | SAOUHSC_00027 | none confidence group_5287 DNA-directed DNA polymerase family A palm domain-containing protein SAOUHSC_00027 23S rRNA(pseudouridine(1915)-N(3))-methyltransferase RlmH none 35.29 0.91 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=35.29; coverage=0.91 18 50 0.3600 0 50 0.0000 cases (MRSA) 3.63 57.4923 3.348-987.4 3.3475 987.412 1.48e-05 13.6750 Panaroo/Bakta+GenBank nucleotide_similarity 33691..34170 matched_representative_sequence=group_5287 BBHJIH_02598;CCGLPJ_01546;CNMMKL_01938;DGCAMH_01216;DHHPLE_02459;DPEBLA_01168;EBFKMK_01392;GNNCOP_01021;HBKHOP_02601;JHLLHD_02608;JPKDEA_02602;KBDKBJ_02554;LPHLDL_02466;NNICCC_00254;NPGDHH_01379;OAHHLH_06597;OMNKFL_02672;PJCLAL_02179 23S rRNA(pseudouridine(1915)-N(3))-methyltransferase RlmH
36 group_5286 gene_presence_absence group_5286 group_5286 | SAOUHSC_03002 | none confidence group_5286 N-glycosyltransferase SAOUHSC_03002 N-glycosyltransferase none 25.45 4.30 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=25.45; coverage=4.30 18 50 0.3600 0 50 0.0000 cases (MRSA) 3.63 57.4923 3.348-987.4 3.3475 987.412 1.48e-05 13.6750 Panaroo/Bakta+GenBank nucleotide_similarity 2775174..2776412 matched_representative_sequence=group_5286 BBHJIH_02597;CCGLPJ_01545;CNMMKL_01937;DGCAMH_01215;DHHPLE_02458;DPEBLA_01169;EBFKMK_01391;GNNCOP_01022;HBKHOP_02600;JHLLHD_02607;JPKDEA_02603;KBDKBJ_02555;LPHLDL_02465;NNICCC_00255;NPGDHH_01380;OAHHLH_06598;OMNKFL_02673;PJCLAL_02180 N-glycosyltransferase
37 group_5100 gene_presence_absence group_5100 group_5100 | SAOUHSC_02531 | none confidence group_5100 SF3 helicase domain-containing protein SAOUHSC_02531 hypothetical protein none 26.54 1.03 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=26.54; coverage=1.03 18 50 0.3600 0 50 0.0000 cases (MRSA) 3.63 57.4923 3.348-987.4 3.3475 987.412 1.48e-05 13.6750 Panaroo/Bakta+GenBank nucleotide_similarity 2333690..2334901 matched_representative_sequence=group_5100 BBHJIH_02596;CCGLPJ_01544;CNMMKL_01936;DGCAMH_01214;DHHPLE_02457;DPEBLA_01170;EBFKMK_01390;GNNCOP_01023;HBKHOP_02599;JHLLHD_02606;JPKDEA_02604;KBDKBJ_02556;LPHLDL_02464;NNICCC_00256;NPGDHH_01381;OAHHLH_06599;OMNKFL_02674;PJCLAL_02181 hypothetical protein
38 group_320 gene_presence_absence ccrC group_320 | SAOUHSC_01273 | none confidence ccrC Staphylococcal casette chromosome site specific recombinase CcrC SAOUHSC_01273 mutL DNA mismatch repair protein none 99.15 34.13 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=99.15; coverage=34.13 18 50 0.3600 0 50 0.0000 cases (MRSA) 3.63 57.4923 3.348-987.4 3.3475 987.412 1.48e-05 13.6750 Panaroo/Bakta+GenBank nucleotide_similarity 1229312..1231321 matched_representative_sequence=group_3205 BBHJIH_02594;CCGLPJ_01542;CNMMKL_01935;DGCAMH_01212;DHHPLE_02455;DPEBLA_01171;EBFKMK_01388;GNNCOP_01025;HBKHOP_02597;JHLLHD_02604;JPKDEA_02606;KBDKBJ_02557;LPHLDL_02462;NNICCC_00257;NPGDHH_01382;OAHHLH_06601;OMNKFL_02676;PJCLAL_02183 DNA mismatch repair protein
39 group_880 gene_presence_absence group_880 group_880 | SAOUHSC_00003 | none confidence group_880 hypothetical protein SAOUHSC_00003 hypothetical protein none 39.53 11.83 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=39.53; coverage=11.83 18 50 0.3600 0 50 0.0000 cases (MRSA) 3.63 57.4923 3.348-987.4 3.3475 987.412 1.58e-05 13.6466 Panaroo/Bakta+GenBank nucleotide_similarity 3670..3915 matched_representative_sequence=group_8805 BBHJIH_02618;CCGLPJ_01530;CNMMKL_01922;DGCAMH_02706;DHHPLE_02443;EBFKMK_01376;FJPBEI_02133;GNNCOP_02694;HBKHOP_02622;JHLLHD_02649;JPKDEA_02620;KBDKBJ_02754;LPHLDL_02450;NNICCC_00269;NPGDHH_02731;OAHHLH_06614;OMNKFL_02689;PJCLAL_02762 hypothetical protein
40 group_5703 gene_presence_absence ;tnp group_5703 | no_reference_locus | none confidence ;tnp hypothetical protein;IS6 family IS431mec transposase none Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. no sequence identity/coverage evidence available 17 50 0.3400 0 50 0.0000 cases (MRSA) 3.55 52.7612 3.068-907.5 3.06753 907.486 3.37e-05 13.1938 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. BBHJIH_02621;CCGLPJ_01533;CNMMKL_01925;DGCAMH_02709;DHHPLE_02446;EBFKMK_01379;FJPBEI_02136;HBKHOP_02625;JHLLHD_02652;JPKDEA_02623;LPHLDL_02453;MGNIJD_00601;NKBKLH_02725;NNICCC_00266;OAHHLH_06611;OMNKFL_02692;PJCLAL_02765 hypothetical protein;IS6 family IS431mec transposase
41 group_5119 gene_presence_absence group_5119 group_5119 | no_reference_locus | none confidence group_5119 Phage protein;hypothetical protein none No confident reference gene assignment; report the stable Panaroo cluster ID. no sequence identity/coverage evidence available 43 50 0.8600 13 50 0.2600 cases (MRSA) 2.41 16.1111 5.964-43.52 5.96413 43.5215 1.26e-06 12.9096 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. AAFANJ_02602;AGNJKP_02366;BBHJIH_02139;BGHJOB_02213;CKFMFB_01054;CNMMKL_00098;DBPPGI_02334;DGCAMH_02751;DHHPLE_02136;DPEBLA_01882;EAMBND_02595;EBFKMK_02739;EBHIAF_01862;EDBMEK_00445;EFOOKO_02377;FCNEHE_02077;FHJCBG_02295;FHPENM_01770;FIIBJA_02048;FJPBEI_02971;FMAEJP_02036;FMOEEE_00559;GEIAPO_02536;GGEFGC_02304;GGOGND_02263;GHNMBF_02185;GLHECH_01366;GNKNJO_02376;GNNCOP_01034;HBKHOP_02227 Phage protein;hypothetical protein
42 group_1274 gene_presence_absence group_1274 group_1274 | SAOUHSC_02194 | none confidence group_1274 hypothetical protein;DEAD/DEAH box helicase domain protein SAOUHSC_02194 HK97 family phage portal protein none 18.58 0.88 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=18.58; coverage=0.88 16 50 0.3200 0 50 0.0000 cases (MRSA) 3.44 48.3043 2.803-832.3 2.80349 832.287 6.55e-05 12.7778 Panaroo/Bakta+GenBank nucleotide_similarity complement(2053915..2055105) matched_representative_sequence=group_1274 BBHJIH_02390;CCGLPJ_01140;CNMMKL_01944;DGCAMH_01207;DHHPLE_02432;EBFKMK_01365;HBKHOP_02437;JHLLHD_02321;JPKDEA_02388;KBDKBJ_02549;LPHLDL_02439;NNICCC_00248;NPGDHH_01374;OAHHLH_06626;OMNKFL_02462;PJCLAL_01206 HK97 family phage portal protein
43 group_5422 gene_presence_absence group_5422 group_5422 | SAOUHSC_00378 | none confidence group_5422 Transposase;hypothetical protein SAOUHSC_00378 hypothetical protein none 82.16 14.54 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=82.16; coverage=14.54 32 50 0.6400 5 50 0.1000 cases (MRSA) 2.61 14.5332 5.071-41.65 5.07059 41.6546 1.61e-06 12.6545 Panaroo/Bakta+GenBank nucleotide_similarity complement(385390..385662) matched_representative_sequence=group_5422 BBHJIH_00004;BCINDJ_00004;BGHJOB_02841;DBPPGI_00361;DHHPLE_01200;DPEBLA_02232;EAMBND_02306;EBHIAF_02014;EDBMEK_00359;EEPHOB_00544;EFOOKO_02253;FCNEHE_02270;FHPENM_00374;FJPBEI_01778;FMOEEE_02300;GGEFGC_00361;GGOGND_00760;GHNMBF_00360;GNKNJO_02247;HBKHOP_01199;HGFBEP_02418;HJFIGM_00649;HJGKNO_00359;IHKMFK_01004;ILJMML_00391;JHLLHD_01084;JPKDEA_00657;KOFDAJ_02557;LPHLDL_01233;NBILEO_02582 hypothetical protein
44 group_2369 gene_presence_absence group_2369 group_2369 | SAOUHSC_00645 | none confidence group_2369 Phage protein;hypothetical protein SAOUHSC_00645 glycerol-3-phosphate cytidylyltransferase none 45.11 7.35 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=45.11; coverage=7.35 47 50 0.9400 19 50 0.3800 cases (MRSA) 2.69 21.9231 6.448-74.53 6.44846 74.5327 6.61e-06 12.6342 Panaroo/Bakta+GenBank nucleotide_similarity 634015..634413 matched_representative_sequence=12_refound_28 12_refound_28;14_refound_42_pseudo;27_refound_124;60_refound_391;62_refound_406_pseudo;63_refound_416;70_refound_454;74_refound_476_pseudo;75_refound_483;76_refound_492_pseudo;77_refound_504_pseudo;82_refound_524;84_refound_542;85_refound_546;86_refound_553;87_refound_557;94_refound_596;95_refound_603_pseudo;AAFANJ_02585;ADDHAP_02084;BCINDJ_02212;BGHJOB_02234;CCGLPJ_01814;CNMMKL_00117;DBPPGI_02561;DGCAMH_02340;DPEBLA_01896;EAMBND_02611;EBFKMK_02687;EBHIAF_01881 glycerol-3-phosphate cytidylyltransferase
45 group_1360 gene_presence_absence SAOUHSC_01932-like (group_1360) group_1360 | SAOUHSC_01932 | low confidence group_1360 Restriction endonuclease subunit S SAOUHSC_01932 type I restriction-modification system subunitS low 66.78 51.06 Low-confidence locus-level GenBank rescue. identity=66.78; coverage=51.06 20 50 0.4000 1 50 0.0200 cases (MRSA) 2.83 22.1803 3.979-123.6 3.97912 123.637 9.29e-06 12.5032 Panaroo/Bakta+GenBank nucleotide_similarity complement(1839335..1840534) matched_representative_sequence=60_refound_388 59_refound_383_pseudo;60_refound_388;82_refound_522;84_refound_538;89_refound_565_pseudo;90_refound_569_pseudo;94_refound_593;BGHJOB_02837;DPEBLA_02379;EDBMEK_00363;EFOOKO_02257;FHPENM_00378;FMOEEE_02296;GGOGND_00764;GHNMBF_00364;HFICCC_03178;HJGKNO_00363;ILJMML_00395;NJAOBP_04458;NKBKLH_02759;NMHDHA_00365 type I restriction-modification system subunitS
46 ptpB gene_presence_absence SAOUHSC_02356 (ptpB) ptpB | SAOUHSC_02356 | high confidence ptpB Low molecular weight protein-tyrosine-phosphatase PtpB SAOUHSC_02356 hypothetical protein high 99.64 99.05 High-confidence locus-level GenBank rescue. identity=99.64; coverage=99.05 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(2178210..2178629) matched_representative_sequence=ptpB AAFANJ_02220;ADDHAP_02387;AGNJKP_02258;BBHJIH_02337;BCINDJ_02438;BGHJOB_02499;BLNHMO_02421;CCGLPJ_02487;CDDCHJ_02368;CIALCM_02439;CJJPLC_02292;CKFMFB_01686;CNMMKL_02025;DBPPGI_02124;DGCAMH_02399;DHHPLE_02334;DNJFEH_01679;DPEBLA_02043;EAMBND_01697;EBFKMK_02217;EBHIAF_02413;EDBMEK_02157;EEPHOB_02119;EFOOKO_02102;EOFOFH_02418;FDFIHM_02495;FHJCBG_02190;FHPENM_02514;FIIBJA_02422;FJPBEI_01472 hypothetical protein
47 group_8769 gene_presence_absence group_8769 group_8769 | SAOUHSC_00012 | none confidence group_8769 hypothetical protein SAOUHSC_00012 hypothetical protein none 29.08 5.98 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=29.08; coverage=5.98 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 15414..15743 matched_representative_sequence=group_8769 AAFANJ_00311;ADDHAP_00693;AGNJKP_01682;BBHJIH_00354;BCINDJ_00446;BGHJOB_01007;BLNHMO_01113;CCGLPJ_00860;CDDCHJ_01838;CIALCM_00718;CJJPLC_01205;CKFMFB_00530;CNMMKL_01311;DBPPGI_00012;DGCAMH_00546;DHHPLE_00851;DNJFEH_00046;DPEBLA_00303;EAMBND_01898;EBFKMK_00438;EBHIAF_01349;EDBMEK_00012;EEPHOB_00894;EFOOKO_01188;EOFOFH_00283;FDFIHM_01176;FHJCBG_01665;FHPENM_00028;FIIBJA_00043;FJPBEI_01847 hypothetical protein
48 group_4339 gene_presence_absence group_4339 group_4339 | SAOUHSC_01918 | none confidence group_4339 Putative lipoprotein;Endonuclease SAOUHSC_01918 hypothetical protein none 85.94 8.46 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=85.94; coverage=8.46 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 1826667..1827317 matched_representative_sequence=group_4339 AAFANJ_02368;ADDHAP_02255;AGNJKP_01978;BBHJIH_00010;BCINDJ_00010;BGHJOB_02850;BLNHMO_02281;CCGLPJ_02339;CDDCHJ_02465;CIALCM_02299;CJJPLC_02179;CKFMFB_02034;CNMMKL_01657;DBPPGI_00353;DGCAMH_02115;DHHPLE_01194;DNJFEH_02349;DPEBLA_02224;EAMBND_02314;EBFKMK_00096;EBHIAF_02020;EDBMEK_00351;EEPHOB_00550;EFOOKO_02245;EOFOFH_02303;FDFIHM_02355;FHJCBG_02003;FHPENM_00366;FIIBJA_02509;FJPBEI_01772 hypothetical protein
49 group_4309 gene_presence_absence group_4309 group_4309 | SAOUHSC_01123 | none confidence group_4309 DNA-binding protein SAOUHSC_01123 hypothetical protein none 81.69 10.95 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=81.69; coverage=10.95 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 1078148..1078372 matched_representative_sequence=group_4309 AAFANJ_00605;ADDHAP_00179;AGNJKP_01059;BBHJIH_00642;BCINDJ_02571;BGHJOB_00608;BLNHMO_00037;CCGLPJ_00565;CDDCHJ_00086;CIALCM_01339;CJJPLC_00904;CKFMFB_01869;CNMMKL_02511;DBPPGI_01070;DGCAMH_00250;DHHPLE_00562;DNJFEH_02718;DPEBLA_01326;EAMBND_00432;EBFKMK_00733;EBHIAF_01088;EDBMEK_01071;EEPHOB_02506;EFOOKO_01696;EOFOFH_00577;FDFIHM_00101;FHJCBG_00443;FHPENM_01152;FIIBJA_00337;FJPBEI_02491 hypothetical protein
50 group_4304 gene_presence_absence sdpA; group_4304 | SAOUHSC_01900 | none confidence sdpA; CPBP family intramembrane metalloprotease SdpA;hypothetical protein SAOUHSC_01900 hypothetical protein none 73.27 2.67 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=73.27; coverage=2.67 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 1810087..1810722 matched_representative_sequence=group_4304 AAFANJ_02387;ADDHAP_02273;AGNJKP_01963;BBHJIH_00027;BCINDJ_00028;BGHJOB_02434;BLNHMO_02265;CCGLPJ_02321;CDDCHJ_01424;CIALCM_02283;CJJPLC_02195;CKFMFB_02019;CNMMKL_01642;DBPPGI_00337;DGCAMH_02097;DHHPLE_01177;DNJFEH_02365;DPEBLA_02209;EAMBND_02335;EBFKMK_00114;EBHIAF_02038;EDBMEK_00336;EEPHOB_00568;EFOOKO_00863;EOFOFH_02321;FDFIHM_02339;FHJCBG_01988;FHPENM_00351;FIIBJA_02490;FJPBEI_02672 hypothetical protein
51 group_4060 gene_presence_absence group_4060 group_4060 | SAOUHSC_00606 | none confidence group_4060 DUF4909 domain-containing protein SAOUHSC_00606 hypothetical protein none 19.79 3.11 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=19.79; coverage=3.11 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 597925..599220 matched_representative_sequence=group_4060 AAFANJ_02369;ADDHAP_02256;AGNJKP_01977;BBHJIH_00011;BCINDJ_00011;BGHJOB_02851;BLNHMO_02280;CCGLPJ_02338;CDDCHJ_02466;CIALCM_02298;CJJPLC_02180;CKFMFB_02033;CNMMKL_01656;DBPPGI_00352;DGCAMH_02114;DHHPLE_01193;DNJFEH_02350;DPEBLA_02223;EAMBND_02315;EBFKMK_00097;EBHIAF_02021;EDBMEK_00350;EEPHOB_00551;EFOOKO_02244;EOFOFH_02304;FDFIHM_02354;FHJCBG_02002;FHPENM_00365;FIIBJA_02508;FJPBEI_01771 hypothetical protein
52 group_3636 gene_presence_absence SAOUHSC_00808-like (group_3636) group_3636 | SAOUHSC_00808 | medium confidence group_3636 DUF5067 domain-containing protein;hypothetical protein SAOUHSC_00808 hypothetical protein medium 99.73 77.50 Medium-confidence locus-level GenBank rescue. identity=99.73; coverage=77.50 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(790206..790934) matched_representative_sequence=group_3636 AAFANJ_00954;ADDHAP_01495;AGNJKP_01267;BBHJIH_00929;BBHJIH_00930;BCINDJ_01160;BGHJOB_00302;BLNHMO_00326;CCGLPJ_00276;CDDCHJ_00955;CIALCM_01050;CJJPLC_00615;CKFMFB_01322;CNMMKL_00293;DBPPGI_01660;DGCAMH_01854;DHHPLE_00276;DHHPLE_00277;DNJFEH_01225;DPEBLA_01504;EAMBND_00121;EBFKMK_02120;EBHIAF_00212;EDBMEK_01158;EEPHOB_01527;EFOOKO_00200;EOFOFH_01748;FDFIHM_00390;FHJCBG_00153;FHPENM_01907 hypothetical protein
53 sel26 gene_presence_absence ;sel26 sel26 | SAOUHSC_01705 | none confidence ;sel26 hypothetical protein;staphylococcal enterotoxin type 26;Enterotoxin SAOUHSC_01705 enterotoxin family protein none 87.14 11.07 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=87.14; coverage=11.07 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(1611370..1612074) matched_representative_sequence=sel26 AAFANJ_00155;ADDHAP_00539;AGNJKP_01525;AGNJKP_01526;BBHJIH_00194;BBHJIH_00195;BCINDJ_00201;BCINDJ_00202;BGHJOB_00787;BLNHMO_01488;CCGLPJ_01012;CCGLPJ_01013;CDDCHJ_01255;CIALCM_01497;CJJPLC_01700;CKFMFB_01575;CNMMKL_01828;CNMMKL_01829;DBPPGI_00164;DBPPGI_00165;DGCAMH_00699;DGCAMH_00700;DHHPLE_01009;DHHPLE_01010;DNJFEH_00264;DPEBLA_00083;EAMBND_00272;EBFKMK_00283;EBFKMK_00284;EBHIAF_01504 enterotoxin family protein
54 emp gene_presence_absence ;emp emp | SAOUHSC_00816 | none confidence ;emp Extracellular matrix protein-binding protein emp;extracellular matrix protein-binding adhesin Emp SAOUHSC_00816 extracellular matrix and plasma binding protein none 90.68 7.12 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=90.68; coverage=7.12 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 797866..798888 matched_representative_sequence=emp AAFANJ_00949;ADDHAP_01489;AGNJKP_01262;BBHJIH_00924;BCINDJ_01165;BGHJOB_00307;BLNHMO_00321;CCGLPJ_00281;CDDCHJ_00961;CIALCM_01055;CJJPLC_00620;CKFMFB_01327;CNMMKL_00299;DBPPGI_00792;DGCAMH_01849;DHHPLE_00282;DNJFEH_01220;DPEBLA_02699;EAMBND_00116;EBFKMK_02125;EBHIAF_00206;EDBMEK_01824;EEPHOB_01522;EFOOKO_00195;EOFOFH_01743;FDFIHM_00385;FHJCBG_00158;FHPENM_01691;FIIBJA_00682;FJPBEI_00234 extracellular matrix and plasma binding protein
55 group_2809 gene_presence_absence group_2809 group_2809 | SAOUHSC_00684 | none confidence group_2809 N-acetyltransferase domain-containing protein SAOUHSC_00684 hypothetical protein none 96.64 16.67 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=96.64; coverage=16.67 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 670865..671308 matched_representative_sequence=group_2809 AAFANJ_01084;ADDHAP_01611;AGNJKP_01380;BBHJIH_01044;BCINDJ_01045;BGHJOB_00188;BLNHMO_00441;CCGLPJ_00163;CDDCHJ_00842;CIALCM_00935;CJJPLC_00500;CKFMFB_01208;CNMMKL_00178;DBPPGI_01547;DGCAMH_01967;DHHPLE_00162;DNJFEH_02270;DPEBLA_01615;EAMBND_00257;EBFKMK_02007;EBHIAF_00328;EDBMEK_01271;EEPHOB_01581;EFOOKO_00313;EOFOFH_01860;FDFIHM_00505;FHJCBG_00038;FHPENM_02020;FIIBJA_00817;FJPBEI_00354 hypothetical protein
56 group_2799 gene_presence_absence SAOUHSC_00810-like (group_2799) group_2799 | SAOUHSC_00810 | low confidence group_2799 hypothetical protein;SMODS-associated and fused to various effectors domain-containing protein SAOUHSC_00810 hypothetical protein low 99.23 50.96 Low-confidence locus-level GenBank rescue. identity=99.23; coverage=50.96 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 791533..792054 matched_representative_sequence=group_2799 AAFANJ_00953;ADDHAP_01494;AGNJKP_01266;BBHJIH_00928;BCINDJ_01161;BGHJOB_00303;BLNHMO_00325;CCGLPJ_00277;CDDCHJ_00956;CDDCHJ_00957;CIALCM_01051;CJJPLC_00616;CKFMFB_01323;CNMMKL_00294;CNMMKL_00295;DBPPGI_01661;DGCAMH_01853;DHHPLE_00278;DNJFEH_01224;DPEBLA_02695;EAMBND_00120;EBFKMK_02121;EBHIAF_00211;EDBMEK_01157;EEPHOB_01526;EFOOKO_00199;EOFOFH_01747;FDFIHM_00389;FHJCBG_00154;FHPENM_01906 hypothetical protein
57 group_2757 gene_presence_absence group_2757 group_2757 | SAOUHSC_02957 | none confidence group_2757 hypothetical protein SAOUHSC_02957 hypothetical protein none 95.52 29.35 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=95.52; coverage=29.35 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(2719286..2719486) matched_representative_sequence=group_2757 AAFANJ_01791;ADDHAP_01842;AGNJKP_00218;BBHJIH_01313;BCINDJ_01981;BGHJOB_02018;BLNHMO_00744;CCGLPJ_01672;CDDCHJ_01102;CIALCM_00323;CJJPLC_00131;CKFMFB_02139;CNMMKL_01177;DBPPGI_01274;DGCAMH_01343;DHHPLE_01311;DNJFEH_02207;DPEBLA_01051;EAMBND_00755;EBFKMK_01519;EBHIAF_00621;EDBMEK_01498;EEPHOB_00407;EFOOKO_01327;EOFOFH_01324;FDFIHM_00807;FHJCBG_01221;FHPENM_01369;FIIBJA_01510;FJPBEI_01930 hypothetical protein
58 group_2639 gene_presence_absence SAOUHSC_01134-like (group_2639) group_2639 | SAOUHSC_01134 | low confidence group_2639 DNA-binding protein SAOUHSC_01134 hypothetical protein low 95.09 46.97 Low-confidence locus-level GenBank rescue. identity=95.09; coverage=46.97 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 1087343..1087531 matched_representative_sequence=group_2639 AAFANJ_00594;ADDHAP_00169;AGNJKP_01048;BBHJIH_00632;BCINDJ_02561;BGHJOB_00618;BLNHMO_00027;CCGLPJ_00575;CDDCHJ_00095;CIALCM_01349;CJJPLC_00914;CKFMFB_01879;CNMMKL_02501;DBPPGI_01079;DGCAMH_00260;DHHPLE_00572;DNJFEH_02728;DPEBLA_01316;EAMBND_00442;EBFKMK_00723;EBHIAF_01098;EDBMEK_01062;EEPHOB_02496;EFOOKO_01687;EOFOFH_00567;FDFIHM_00091;FHJCBG_00453;FHPENM_01143;FIIBJA_00326;FJPBEI_02501 hypothetical protein
59 group_2551 gene_presence_absence group_2551 group_2551 | SAOUHSC_02892 | none confidence group_2551 hypothetical protein SAOUHSC_02892 hypothetical protein none 72.51 13.08 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=72.51; coverage=13.08 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 2664225..2664725 matched_representative_sequence=group_2551 AAFANJ_01844;ADDHAP_01895;AGNJKP_00165;BBHJIH_01367;BCINDJ_01532;BGHJOB_01967;BLNHMO_00691;CCGLPJ_01724;CDDCHJ_01051;CIALCM_00376;CJJPLC_00078;CKFMFB_02085;CNMMKL_02458;DBPPGI_01327;DGCAMH_01395;DHHPLE_01365;DNJFEH_01834;DPEBLA_02688;EAMBND_02384;EBFKMK_01571;EBHIAF_00567;EDBMEK_01445;EEPHOB_00461;EFOOKO_01275;EOFOFH_01375;FDFIHM_00754;FHJCBG_01275;FHPENM_01421;FIIBJA_01457;FJPBEI_02179 hypothetical protein
60 group_2387 gene_presence_absence tagX group_2387 | SAOUHSC_00644 | none confidence tagX Putative glycosyltransferase TagX SAOUHSC_00644 glycosyltransferase TagX none 97.74 14.88 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=97.74; coverage=14.88 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 632891..633952 matched_representative_sequence=group_2387 AAFANJ_01120;ADDHAP_01647;AGNJKP_01416;BBHJIH_01080;BCINDJ_01009;BGHJOB_00151;BLNHMO_00477;CCGLPJ_00127;CDDCHJ_00791;CIALCM_00899;CJJPLC_00464;CKFMFB_02422;CNMMKL_00079;DBPPGI_01511;DGCAMH_02003;DHHPLE_00126;DNJFEH_02306;DPEBLA_02523;EAMBND_00912;EBFKMK_01971;EBHIAF_00364;EDBMEK_01307;EEPHOB_01545;EFOOKO_00349;EOFOFH_01896;FDFIHM_00541;FHJCBG_00002;FHPENM_02056;FIIBJA_00853;FJPBEI_00390 glycosyltransferase TagX
61 group_2132 gene_presence_absence group_2132 group_2132 | SAOUHSC_02726 | none confidence group_2132 Bacterial transcription activator effector binding domain-containing protein;hypothetical protein SAOUHSC_02726 hypothetical protein none 96.41 21.31 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=96.41; coverage=21.31 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(2506882..2507355) matched_representative_sequence=group_2132 AAFANJ_01986;ADDHAP_01395;AGNJKP_00026;BBHJIH_01507;BCINDJ_01673;BGHJOB_01891;BLNHMO_02161;CCGLPJ_02010;CDDCHJ_00636;CIALCM_02187;CJJPLC_01511;CKFMFB_00216;CNMMKL_00561;DBPPGI_01726;DGCAMH_01540;DHHPLE_01505;DNJFEH_01317;DPEBLA_01679;EAMBND_01082;EBFKMK_01649;EBHIAF_01756;EDBMEK_01889;EEPHOB_01280;EFOOKO_01994;EOFOFH_01658;FDFIHM_01700;FHJCBG_01417;FHPENM_02396;FIIBJA_01735;FJPBEI_01226 hypothetical protein
62 group_1942 gene_presence_absence group_1942 group_1942 | SAOUHSC_02925 | none confidence group_1942 hypothetical protein SAOUHSC_02925 hypothetical protein none 96.88 21.58 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=96.88; coverage=21.58 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 2691116..2691532 matched_representative_sequence=group_1942 AAFANJ_01812;ADDHAP_01862;AGNJKP_00197;BBHJIH_01334;BCINDJ_01960;BGHJOB_01997;BLNHMO_00723;CCGLPJ_01694;CDDCHJ_01081;CIALCM_00344;CJJPLC_00110;CKFMFB_02118;CNMMKL_01198;DBPPGI_01296;DGCAMH_01365;DHHPLE_01332;DNJFEH_02228;DPEBLA_01029;EAMBND_00733;EBFKMK_01541;EBHIAF_00600;EDBMEK_01476;EEPHOB_00428;EFOOKO_01305;EOFOFH_01345;FDFIHM_00786;FHJCBG_01243;FHPENM_01391;FIIBJA_01489;FJPBEI_02636 hypothetical protein
63 group_1933 gene_presence_absence group_1933 group_1933 | SAOUHSC_01595 | none confidence group_1933 Phage protein SAOUHSC_01595 hypothetical protein none 87.55 12.45 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=87.55; coverage=12.45 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(1520234..1520482) matched_representative_sequence=group_1933 AAFANJ_00255;ADDHAP_00638;AGNJKP_01625;BBHJIH_00298;BCINDJ_00302;BGHJOB_00885;BLNHMO_01389;CCGLPJ_00914;CDDCHJ_01956;CIALCM_01398;CJJPLC_01799;CKFMFB_02477;CNMMKL_01431;DBPPGI_00067;DGCAMH_00600;DHHPLE_00906;DNJFEH_00165;DPEBLA_00181;EAMBND_01762;EBFKMK_00383;EBHIAF_01404;EDBMEK_00067;EEPHOB_00838;EFOOKO_01132;EOFOFH_00227;FDFIHM_01783;FHJCBG_01720;FHPENM_00083;FIIBJA_02117;FJPBEI_02277 hypothetical protein
64 group_1854 gene_presence_absence group_1854 group_1854 | SAOUHSC_02104 | none confidence group_1854 Cytosolic protein SAOUHSC_02104 hypothetical protein none 96.14 19.32 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=96.14; coverage=19.32 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(1978643..1979056) matched_representative_sequence=group_1854 AAFANJ_02433;ADDHAP_02004;AGNJKP_02498;BBHJIH_02252;BCINDJ_02128;BGHJOB_02316;BLNHMO_02000;CCGLPJ_01915;CDDCHJ_02031;CIALCM_02086;CJJPLC_02363;CKFMFB_01169;CNMMKL_01889;DBPPGI_02207;DGCAMH_02240;DHHPLE_02249;DNJFEH_01590;DPEBLA_01979;EAMBND_02112;EBFKMK_02389;EBHIAF_01963;EDBMEK_02243;EEPHOB_01879;EFOOKO_02203;EOFOFH_02053;FDFIHM_02186;FHJCBG_02384;FHPENM_01873;FIIBJA_01948;FJPBEI_02304 hypothetical protein
65 group_1747 gene_presence_absence SAOUHSC_00704-like (group_1747) group_1747 | SAOUHSC_00704 | medium confidence group_1747 Lipoprotein SAOUHSC_00704 hypothetical protein medium 98.47 77.20 Medium-confidence locus-level GenBank rescue. identity=98.47; coverage=77.20 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 688884..689336 matched_representative_sequence=group_1747 AAFANJ_01064;ADDHAP_01591;AGNJKP_01360;BBHJIH_01024;BCINDJ_01065;BGHJOB_00208;BLNHMO_00421;CCGLPJ_00183;CDDCHJ_00862;CIALCM_00955;CJJPLC_00520;CKFMFB_01228;CNMMKL_00198;DBPPGI_01567;DGCAMH_01947;DHHPLE_00182;DNJFEH_02581;DPEBLA_01595;EAMBND_00237;EBFKMK_02027;EBHIAF_00308;EDBMEK_01251;EEPHOB_01602;EFOOKO_00293;EOFOFH_01840;FDFIHM_00485;FHJCBG_00058;FHPENM_02000;FIIBJA_00797;FJPBEI_00334 hypothetical protein
66 group_1673 gene_presence_absence group_1673 group_1673 | SAOUHSC_01764 | none confidence group_1673 Type III leader peptidase family protein SAOUHSC_01764 hypothetical protein none 98.31 22.32 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=98.31; coverage=22.32 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(1663415..1664122) matched_representative_sequence=group_1673 AAFANJ_00102;ADDHAP_00487;AGNJKP_01474;BBHJIH_00141;BCINDJ_00142;BGHJOB_00736;BLNHMO_01541;CCGLPJ_01065;CDDCHJ_01307;CIALCM_01550;CJJPLC_01647;CKFMFB_01629;CNMMKL_00724;DBPPGI_00218;DGCAMH_00752;DHHPLE_01063;DNJFEH_00317;DPEBLA_00029;EAMBND_00325;EBFKMK_00231;EBHIAF_01560;EDBMEK_00217;EEPHOB_00683;EFOOKO_00982;EOFOFH_00075;FDFIHM_01935;FHJCBG_01869;FHPENM_00233;FIIBJA_02270;FJPBEI_00531 hypothetical protein
67 group_1613 gene_presence_absence group_1613 group_1613 | SAOUHSC_02650 | none confidence group_1613 Serine protease HtrA-like SAOUHSC_02650 hypothetical protein none 24.69 0.65 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=24.69; coverage=0.65 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(2436751..2437380) matched_representative_sequence=group_1613 AAFANJ_00746;ADDHAP_00322;AGNJKP_02536;BBHJIH_00785;BCINDJ_01376;BGHJOB_00465;BLNHMO_00178;CCGLPJ_00424;CDDCHJ_02163;CIALCM_01198;CJJPLC_00763;CKFMFB_00853;CNMMKL_00435;DBPPGI_00930;DGCAMH_00110;DHHPLE_00421;DNJFEH_00818;DPEBLA_00869;EAMBND_02177;EBFKMK_00873;EBHIAF_02248;EDBMEK_01686;EEPHOB_01383;EFOOKO_00056;EOFOFH_00717;FDFIHM_00242;FHJCBG_00301;FHPENM_01553;FIIBJA_00477;FJPBEI_01092 hypothetical protein
68 group_1571 gene_presence_absence group_1571 group_1571 | SAOUHSC_00237 | none confidence group_1571 SAM-dependent methyltransferase SAOUHSC_00237 hypothetical protein none 95.54 10.24 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=95.54; coverage=10.24 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(258896..259657) matched_representative_sequence=group_1571 AAFANJ_01451;ADDHAP_00892;AGNJKP_00552;BBHJIH_01923;BCINDJ_00792;BGHJOB_01490;BLNHMO_01061;CCGLPJ_01327;CDDCHJ_01468;CIALCM_00006;CJJPLC_00449;CKFMFB_00645;CNMMKL_01032;DBPPGI_00601;DGCAMH_01020;DHHPLE_01938;DNJFEH_00326;DPEBLA_00618;EAMBND_00616;EBFKMK_01178;EBHIAF_00948;EDBMEK_00637;EEPHOB_00107;EFOOKO_00663;EOFOFH_01018;FDFIHM_01124;FHJCBG_00921;FHPENM_00726;FIIBJA_01167;FJPBEI_01887 hypothetical protein
69 scdA gene_presence_absence scdA scdA | SAOUHSC_00229 | none confidence scdA Iron-sulfur cluster repair protein ScdA SAOUHSC_00229 cell wall biosynthesis protein ScdA none 98.81 26.67 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=98.81; coverage=26.67 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 250591..251265 matched_representative_sequence=scdA AAFANJ_01460;ADDHAP_00900;AGNJKP_00542;BBHJIH_01914;BCINDJ_00801;BGHJOB_01481;BLNHMO_01052;CCGLPJ_01318;CDDCHJ_01459;CIALCM_00015;CJJPLC_00440;CKFMFB_00635;CNMMKL_01022;DBPPGI_00609;DGCAMH_01029;DHHPLE_01947;DNJFEH_00335;DPEBLA_00626;EAMBND_00625;EBFKMK_01187;EBHIAF_00939;EDBMEK_00629;EEPHOB_00115;EFOOKO_00655;EOFOFH_01027;FDFIHM_01115;FHJCBG_00931;FHPENM_00734;FIIBJA_01158;FJPBEI_01896 cell wall biosynthesis protein ScdA
70 group_1455 gene_presence_absence group_1455 group_1455 | SAOUHSC_02973 | none confidence group_1455 Low-complexity protein;hypothetical protein SAOUHSC_02973 hypothetical protein none 65.17 6.12 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=65.17; coverage=6.12 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 2735412..2735870 matched_representative_sequence=group_1455 AAFANJ_01776;ADDHAP_01827;AGNJKP_00233;BBHJIH_01298;BCINDJ_01996;BGHJOB_02033;BLNHMO_00759;CCGLPJ_01657;CDDCHJ_01118;CIALCM_00308;CJJPLC_00146;CKFMFB_02154;CNMMKL_01162;DBPPGI_01258;DGCAMH_01328;DHHPLE_01296;DNJFEH_00998;DPEBLA_01066;EAMBND_00770;EBFKMK_01504;EBHIAF_00637;EDBMEK_01513;EEPHOB_00392;EFOOKO_01342;EOFOFH_01309;FDFIHM_00822;FHJCBG_01206;FHPENM_01354;FIIBJA_01525;FJPBEI_01946 hypothetical protein
71 group_1350 gene_presence_absence group_1350 group_1350 | SAOUHSC_01638 | none confidence group_1350 Competence protein ComGE SAOUHSC_01638 hypothetical protein none 94.69 30.00 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=94.69; coverage=30.00 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(1557239..1557559) matched_representative_sequence=group_1350 AAFANJ_00215;ADDHAP_00600;AGNJKP_01585;BBHJIH_00255;BCINDJ_00262;BGHJOB_00847;BLNHMO_01428;CCGLPJ_00952;CDDCHJ_01995;CIALCM_01437;CJJPLC_01760;CKFMFB_01515;CNMMKL_01766;DBPPGI_00105;DGCAMH_00638;DHHPLE_00949;DNJFEH_00204;DPEBLA_00143;EAMBND_01800;EBFKMK_00345;EBHIAF_01444;EDBMEK_00105;EEPHOB_00798;EFOOKO_01094;EOFOFH_00189;FDFIHM_01822;FHJCBG_01758;FHPENM_00121;FIIBJA_02157;FJPBEI_00409 hypothetical protein
72 group_1246 gene_presence_absence SAOUHSC_02129-like (group_1246) group_1246 | SAOUHSC_02129 | low confidence group_1246 Staphostatin A domain-containing protein SAOUHSC_02129 hypothetical protein low 98.17 42.51 Low-confidence locus-level GenBank rescue. identity=98.17; coverage=42.51 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 2003536..2003862 matched_representative_sequence=group_1246 AAFANJ_02454;ADDHAP_02025;AGNJKP_02477;BBHJIH_02231;BCINDJ_02149;BGHJOB_02295;BLNHMO_02021;CCGLPJ_01875;CDDCHJ_02052;CIALCM_02065;CJJPLC_02384;CKFMFB_01145;CNMMKL_01868;DBPPGI_02228;DGCAMH_02280;DHHPLE_02228;DNJFEH_01611;DPEBLA_01958;EAMBND_02134;EBFKMK_02429;EBHIAF_01942;EDBMEK_02264;EEPHOB_01900;EFOOKO_02182;EOFOFH_02074;FDFIHM_02207;FHJCBG_02405;FHPENM_01852;FIIBJA_01969;FJPBEI_01688 hypothetical protein
73 group_1203 gene_presence_absence ;vraA group_1203 | SAOUHSC_00144 | none confidence ;vraA hypothetical protein;Putative long chain fatty acid-CoA ligase VraA SAOUHSC_00144 hypothetical protein none 98.09 4.39 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=98.09; coverage=4.39 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 149045..156220 matched_representative_sequence=group_1203 AAFANJ_01534;ADDHAP_00974;AGNJKP_00460;BBHJIH_01833;BCINDJ_00882;BGHJOB_01407;BLNHMO_00966;CCGLPJ_01243;CDDCHJ_01782;CIALCM_00101;CJJPLC_00354;CKFMFB_00560;CNMMKL_01291;DBPPGI_00684;DGCAMH_01104;DHHPLE_02028;DNJFEH_00422;DPEBLA_00708;EAMBND_00700;EBFKMK_01262;EBHIAF_00856;EDBMEK_00554;EEPHOB_00196;EFOOKO_00580;EOFOFH_01102;FDFIHM_01029;FHJCBG_01005;FHPENM_00809;FIIBJA_01084;FJPBEI_00856 hypothetical protein
74 group_894 gene_presence_absence panB group_894 | SAOUHSC_02919 | none confidence panB 3-methyl-2-oxobutanoatehydroxymethyltransferase SAOUHSC_02919 panB 3-methyl-2-oxobutanoatehydroxymethyltransferase none 39.73 2.26 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=39.73; coverage=2.26 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(2683527..2684318) matched_representative_sequence=group_8942 AAFANJ_02109;ADDHAP_01275;AGNJKP_01833;BBHJIH_01628;BCINDJ_01793;BGHJOB_01767;BLNHMO_01759;CCGLPJ_02131;CDDCHJ_00516;CIALCM_01691;CJJPLC_01393;CKFMFB_00096;CNMMKL_01539;DBPPGI_01935;DGCAMH_01661;DHHPLE_01626;DNJFEH_00559;DPEBLA_01439;EAMBND_01361;EBFKMK_01770;EBHIAF_01636;EDBMEK_02087;EEPHOB_01158;EFOOKO_01798;EOFOFH_01537;FDFIHM_01582;FHJCBG_01539;FHPENM_02084;FIIBJA_01858;FJPBEI_00627 3-methyl-2-oxobutanoatehydroxymethyltransferase
75 scpA gene_presence_absence scpA scpA | SAOUHSC_02127 | none confidence scpA cysteine protease staphopain A SAOUHSC_02127 staphopain thiol proteinase none 98.29 13.02 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=98.29; coverage=13.02 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 2002339..2003505 matched_representative_sequence=scpA AAFANJ_02453;ADDHAP_02024;AGNJKP_02478;BBHJIH_02232;BCINDJ_02148;BGHJOB_02296;BLNHMO_02020;CCGLPJ_01876;CDDCHJ_02051;CIALCM_02066;CJJPLC_02383;CKFMFB_01146;CNMMKL_01869;DBPPGI_02227;DGCAMH_02279;DHHPLE_02229;DNJFEH_01610;DPEBLA_01959;EAMBND_02133;EBFKMK_02428;EBHIAF_01943;EDBMEK_02263;EEPHOB_01899;EFOOKO_02183;EOFOFH_02073;FDFIHM_02206;FHJCBG_02404;FHPENM_01853;FIIBJA_01968;FJPBEI_01687 staphopain thiol proteinase
76 group_763 gene_presence_absence SAOUHSC_01622 (group_763) group_763 | SAOUHSC_01622 | high confidence group_763 hypothetical protein SAOUHSC_01622 hypothetical protein high 100.00 100.00 High-confidence locus-level GenBank rescue. identity=100.00; coverage=100.00 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_exact_or_contained complement(1544951..1545313) matched_representative_sequence=group_7635 AAFANJ_00024;ADDHAP_02315;AGNJKP_01927;BBHJIH_00064;BCINDJ_00065;BGHJOB_02393;BLNHMO_02224;CCGLPJ_02281;CDDCHJ_01386;CIALCM_02242;CJJPLC_02236;CKFMFB_02633;CNMMKL_00804;DBPPGI_00299;DGCAMH_02057;DHHPLE_01140;DNJFEH_02529;DPEBLA_02172;EAMBND_00404;EBFKMK_00154;EBHIAF_02097;EDBMEK_00298;EEPHOB_00605;EFOOKO_00901;EOFOFH_02361;FDFIHM_02298;FHJCBG_01949;FHPENM_00313;FIIBJA_02348;FJPBEI_02081 hypothetical protein
77 group_750 gene_presence_absence rpsI group_750 | SAOUHSC_02477 | none confidence rpsI 30S ribosomal protein S9 SAOUHSC_02477 rpsI 30S ribosomal protein S9 none 89.14 7.38 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=89.14; coverage=7.38 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(2299327..2299725) matched_representative_sequence=group_7500 AAFANJ_00149;ADDHAP_00535;AGNJKP_01521;BBHJIH_00188;BCINDJ_00195;BGHJOB_00782;BLNHMO_01494;CCGLPJ_01018;CDDCHJ_01259;CIALCM_01503;CJJPLC_01694;CKFMFB_01582;CNMMKL_01834;DBPPGI_00170;DGCAMH_00705;DHHPLE_01016;DNJFEH_00270;DPEBLA_00076;EAMBND_00278;EBFKMK_00278;EBHIAF_01512;EDBMEK_00170;EEPHOB_00731;EFOOKO_01029;EOFOFH_00122;FDFIHM_01888;FHJCBG_01822;FHPENM_00186;FIIBJA_02223;FJPBEI_00477 30S ribosomal protein S9
78 group_704 gene_presence_absence SAOUHSC_00659 (group_704) group_704 | SAOUHSC_00659 | high confidence group_704 YueH-like family protein SAOUHSC_00659 hypothetical protein high 100.00 100.00 High-confidence locus-level GenBank rescue. identity=100.00; coverage=100.00 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_exact_or_contained 646350..646847 matched_representative_sequence=group_7048 AAFANJ_00749;ADDHAP_00325;AGNJKP_02533;BBHJIH_00788;BCINDJ_01373;BGHJOB_00462;BLNHMO_00181;CCGLPJ_00421;CDDCHJ_02160;CIALCM_01195;CJJPLC_00760;CKFMFB_00856;CNMMKL_00432;DBPPGI_00927;DGCAMH_00107;DHHPLE_00418;DNJFEH_00821;DPEBLA_00866;EAMBND_02174;EBFKMK_00876;EBHIAF_02251;EDBMEK_01689;EEPHOB_01386;EFOOKO_00059;EOFOFH_00720;FDFIHM_00245;FHJCBG_00298;FHPENM_01556;FIIBJA_00480;FJPBEI_01095 hypothetical protein
79 group_5389 gene_presence_absence group_5389 group_5389 | SAOUHSC_00094 | none confidence group_5389 Phage protein;hypothetical protein SAOUHSC_00094 hypothetical protein none 22.03 1.01 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=22.03; coverage=1.01 15 50 0.3000 0 50 0.0000 cases (MRSA) 3.35 44.0986 2.554-761.4 2.55406 761.408 0.00014 12.3165 Panaroo/Bakta+GenBank nucleotide_similarity 100455..101054 matched_representative_sequence=group_5389 BBHJIH_02599;CCGLPJ_01547;DGCAMH_01217;DGCAMH_01218;DHHPLE_02460;EBFKMK_01393;EBFKMK_01394;GNNCOP_01020;HBKHOP_02602;JHLLHD_02609;JPKDEA_02601;KBDKBJ_02553;LPHLDL_02467;NPGDHH_01378;OAHHLH_06596;OMNKFL_02671;PJCLAL_02178 hypothetical protein
80 group_3396 gene_presence_absence ;rinB group_3396 | SAOUHSC_02053 | low confidence ;rinB hypothetical protein;RinB SAOUHSC_02053 transcriptional activator rinb-like protein low 79.06 44.00 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=79.06; coverage=44.00 39 50 0.7800 10 50 0.2000 cases (MRSA) 2.26 13.2484 5.152-34.07 5.15212 34.0678 2.67e-06 12.3012 Panaroo/Bakta+GenBank nucleotide_similarity complement(1951266..1951454) matched_representative_sequence=group_3396 AGNJKP_02347;BBHJIH_02159;BCINDJ_02213;BGHJOB_02233;CCGLPJ_01813;CNMMKL_00116;DBPPGI_02562;DGCAMH_02341;DHHPLE_02156;DPEBLA_01893;EBFKMK_02688;EDBMEK_02504;EFOOKO_02529;EOFOFH_02135;FHPENM_01789;FJPBEI_01751;FMAEJP_02020;GEIAPO_02552;GGEFGC_02533;GGOGND_02241;GHNMBF_02165;GNFCHG_02499;GNKNJO_02350;GNNCOP_01417;HBKHOP_02207;HFICCC_03524;HJFIGM_02017;HJGKNO_02392;IGAMFP_02138;ILJMML_02525 transcriptional activator rinb-like protein
81 group_8659 gene_presence_absence SAOUHSC_02190 (group_8659) group_8659 | SAOUHSC_02190 | high confidence group_8659 Bacteriophage SAOUHSC_02190 hypothetical protein high 100.00 100.00 High-confidence locus-level GenBank rescue. identity=100.00; coverage=100.00 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_exact_or_contained complement(2051809..2051967) matched_representative_sequence=group_8659 AGNJKP_02334;BBHJIH_02172;CKFMFB_01087;DBPPGI_02551;DHHPLE_02169;DPEBLA_01906;EAMBND_02521;EDBMEK_02493;EFOOKO_02540;FHJCBG_02266;FHPENM_01800;FMOEEE_02662;GGEFGC_02544;GHNMBF_02154;GNKNJO_02593;HBKHOP_02194;HFICCC_03513;HGAGGM_02639;HJGKNO_02381;ILJMML_02536;JHLLHD_02046;JPKDEA_02077;KOFDAJ_02494;LPHLDL_02198;MGNIJD_02516;NBILEO_02519;NCJOOM_02763;NJAOBP_03642;NPGDHH_02382;OAHHLH_04861 hypothetical protein
82 group_7790 gene_presence_absence SAOUHSC_02189-like (group_7790) group_7790 | SAOUHSC_02189 | medium confidence group_7790 DNA packaging protein SAOUHSC_02189 hypothetical protein medium 99.40 60.96 Medium-confidence locus-level GenBank rescue. identity=99.40; coverage=60.96 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(2051468..2051800) matched_representative_sequence=group_7790 AGNJKP_02333;BBHJIH_02173;CKFMFB_01088;DBPPGI_02550;DHHPLE_02170;DPEBLA_01907;EAMBND_02520;EDBMEK_02492;EFOOKO_02541;FHJCBG_02265;FHPENM_01801;FMOEEE_02663;GGEFGC_02545;GHNMBF_02153;GNKNJO_02594;HBKHOP_02193;HFICCC_03512;HGAGGM_02640;HJGKNO_02380;ILJMML_02537;JHLLHD_02045;JPKDEA_02076;KOFDAJ_02493;LPHLDL_02197;MGNIJD_02515;NBILEO_02518;NCJOOM_02762;NJAOBP_03643;NPGDHH_02381;OAHHLH_04860 hypothetical protein
83 group_7782 gene_presence_absence SAOUHSC_02188 (group_7782) group_7782 | SAOUHSC_02188 | high confidence group_7782 Head-tail adaptor SAOUHSC_02188 phage head-tail adaptor high 100.00 100.00 High-confidence locus-level GenBank rescue. identity=100.00; coverage=100.00 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_exact_or_contained complement(2051146..2051481) matched_representative_sequence=group_7782 AGNJKP_02332;BBHJIH_02174;CKFMFB_01089;DBPPGI_02549;DHHPLE_02171;DPEBLA_01908;EAMBND_02519;EDBMEK_02491;EFOOKO_02542;FHJCBG_02264;FHPENM_01802;FMOEEE_02664;GGEFGC_02546;GHNMBF_02152;GNKNJO_02595;HBKHOP_02192;HFICCC_03511;HGAGGM_02641;HJGKNO_02379;ILJMML_02538;JHLLHD_02044;JPKDEA_02075;KOFDAJ_02492;LPHLDL_02196;MGNIJD_02514;NBILEO_02517;NCJOOM_02761;NJAOBP_03644;NPGDHH_02380;OAHHLH_04859 phage head-tail adaptor
84 group_6751 gene_presence_absence SAOUHSC_02193 (group_6751) group_6751 | SAOUHSC_02193 | high confidence group_6751 Prohead protease SAOUHSC_02193 prohead protease high 100.00 100.00 High-confidence locus-level GenBank rescue. identity=100.00; coverage=100.00 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_exact_or_contained complement(2053338..2053922) matched_representative_sequence=group_6751 63_refound_409_pseudo;AGNJKP_02336;BBHJIH_02170;CKFMFB_01085;DBPPGI_02553;DHHPLE_02167;DPEBLA_01904;EAMBND_02523;EDBMEK_02495;EFOOKO_02538;FHJCBG_02268;FHPENM_01798;FMOEEE_02660;GGEFGC_02542;GHNMBF_02156;GNKNJO_02591;HBKHOP_02196;HFICCC_03515;HGAGGM_02637;HJGKNO_02383;ILJMML_02534;JHLLHD_02048;JPKDEA_02079;KOFDAJ_02496;LPHLDL_02200;MGNIJD_02518;NBILEO_02521;NJAOBP_03640;NPGDHH_02384;OAHHLH_04863 prohead protease
85 group_3641 gene_presence_absence group_3641 group_3641 | SAOUHSC_02185 | none confidence group_3641 BIG2 domain-containing protein;hypothetical protein SAOUHSC_02185 phi PVL orf 13-like protein none 87.53 5.56 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=87.53; coverage=5.56 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(2049438..2050391) matched_representative_sequence=group_3641 AGNJKP_02329;BBHJIH_02177;CKFMFB_01092;DBPPGI_02546;DHHPLE_02174;DPEBLA_01911;EAMBND_02516;EDBMEK_02488;EFOOKO_02545;FHJCBG_02261;FHPENM_01805;FMOEEE_02667;GGEFGC_02549;GHNMBF_02149;GNKNJO_02598;HBKHOP_02189;HFICCC_03508;HGAGGM_02644;HJGKNO_02376;ILJMML_02541;JHLLHD_02041;JPKDEA_02072;KOFDAJ_02489;LPHLDL_02193;MGNIJD_02511;NBILEO_02514;NCJOOM_02792;NJAOBP_03647;NPGDHH_02377;OAHHLH_04856 phi PVL orf 13-like protein
86 group_3377 gene_presence_absence group_3377 group_3377 | SAOUHSC_02184 | none confidence group_3377 Phage protein SAOUHSC_02184 phi PVL orf 14-like protein none 94.41 11.86 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=94.41; coverage=11.86 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(2048927..2049373) matched_representative_sequence=group_3377 AGNJKP_02328;BBHJIH_02178;CKFMFB_01093;DBPPGI_02545;DHHPLE_02175;DPEBLA_01912;EAMBND_02515;EDBMEK_02487;EFOOKO_02546;FHJCBG_02260;FHPENM_01806;FMOEEE_02668;GGEFGC_02550;GHNMBF_02148;GNKNJO_02599;HBKHOP_02188;HFICCC_03507;HGAGGM_02645;HJGKNO_02375;ILJMML_02542;JHLLHD_02040;JPKDEA_02071;KOFDAJ_02488;LPHLDL_02192;MGNIJD_02510;NBILEO_02513;NCJOOM_02791;NJAOBP_03648;NPGDHH_02376;OAHHLH_04855 phi PVL orf 14-like protein
87 group_2821 gene_presence_absence group_2821 group_2821 | SAOUHSC_02186 | none confidence group_2821 DUF806 domain-containing protein SAOUHSC_02186 phi PVL orf 12-like protein none 87.66 19.69 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=87.66; coverage=19.69 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(2050392..2050772) matched_representative_sequence=group_2821 AGNJKP_02330;BBHJIH_02176;CKFMFB_01091;DBPPGI_02547;DHHPLE_02173;DPEBLA_01910;EAMBND_02517;EDBMEK_02489;EFOOKO_02544;FHJCBG_02262;FHPENM_01804;FMOEEE_02666;GGEFGC_02548;GHNMBF_02150;GNKNJO_02597;HBKHOP_02190;HFICCC_03509;HGAGGM_02643;HJGKNO_02377;ILJMML_02540;JHLLHD_02042;JPKDEA_02073;KOFDAJ_02490;LPHLDL_02194;MGNIJD_02512;NBILEO_02515;NCJOOM_02759;NJAOBP_03646;NPGDHH_02378;OAHHLH_04857 phi PVL orf 12-like protein
88 group_2329 gene_presence_absence SAOUHSC_02200 (group_2329) group_2329 | SAOUHSC_02200 | high confidence group_2329 Phage protein SAOUHSC_02200 hypothetical protein high 97.21 93.98 High-confidence locus-level GenBank rescue. identity=97.21; coverage=93.98 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(2058606..2059076) matched_representative_sequence=group_2329 AGNJKP_02343;BBHJIH_02163;CKFMFB_01078;DBPPGI_02560;DHHPLE_02160;DPEBLA_01897;EAMBND_02530;EDBMEK_02502;EFOOKO_02531;FHJCBG_02275;FHPENM_01791;FMOEEE_02653;GGEFGC_02535;GHNMBF_02163;GNKNJO_02584;HBKHOP_02203;HFICCC_03522;HGAGGM_02630;HJGKNO_02390;ILJMML_02527;JHLLHD_02055;JPKDEA_02086;KOFDAJ_02503;LPHLDL_02207;MGNIJD_02525;NBILEO_02528;NCJOOM_02777;NJAOBP_03633;NPGDHH_02391;OAHHLH_04870 hypothetical protein
89 group_2300 gene_presence_absence yajD group_2300 | SAOUHSC_02198 | none confidence yajD Putative HNH nuclease YajD SAOUHSC_02198 hypothetical protein none 96.42 26.84 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=96.42; coverage=26.84 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(2057679..2058023) matched_representative_sequence=group_2300 AGNJKP_02341;BBHJIH_02165;CKFMFB_01080;DBPPGI_02558;DHHPLE_02162;DPEBLA_01899;EAMBND_02528;EDBMEK_02500;EFOOKO_02533;FHJCBG_02273;FHPENM_01793;FMOEEE_02655;GGEFGC_02537;GHNMBF_02161;GNKNJO_02586;HBKHOP_02201;HFICCC_03520;HGAGGM_02632;HJGKNO_02388;ILJMML_02529;JHLLHD_02053;JPKDEA_02084;KOFDAJ_02501;LPHLDL_02205;MGNIJD_02523;NBILEO_02526;NCJOOM_02805;NJAOBP_03635;NPGDHH_02389;OAHHLH_04868 hypothetical protein
90 group_1218 gene_presence_absence SAOUHSC_02196-like (group_1218) group_1218 | SAOUHSC_02196 | medium confidence group_1218 hypothetical protein;Terminase large subunit SAOUHSC_02196 phage terminase large subunit medium 99.94 65.19 Medium-confidence locus-level GenBank rescue. identity=99.94; coverage=65.19 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(2055385..2057079) matched_representative_sequence=group_1218 AGNJKP_02339;BBHJIH_02167;CKFMFB_01082;DBPPGI_02556;DHHPLE_02164;DPEBLA_01901;EAMBND_02526;EDBMEK_02498;EFOOKO_02535;FHJCBG_02271;FHPENM_01795;FMOEEE_02657;GGEFGC_02539;GHNMBF_02159;GNKNJO_02588;HBKHOP_02199;HFICCC_03518;HGAGGM_02634;HJGKNO_02386;ILJMML_02531;JHLLHD_02051;JPKDEA_02082;KOFDAJ_02499;LPHLDL_02203;MGNIJD_02521;NBILEO_02524;NCJOOM_02773;NJAOBP_03637;NPGDHH_02387;OAHHLH_04866 phage terminase large subunit
91 group_1183 gene_presence_absence SAOUHSC_02191-like (group_1183) group_1183 | SAOUHSC_02191 | medium confidence group_1183 HK97 family phage major capsid protein SAOUHSC_02191 HK97 family phage major capsid protein medium 99.84 79.57 Medium-confidence locus-level GenBank rescue. identity=99.84; coverage=79.57 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(2052003..2053250) matched_representative_sequence=group_1183 AGNJKP_02335;BBHJIH_02171;CKFMFB_01086;DBPPGI_02552;DHHPLE_02168;DPEBLA_01905;EAMBND_02522;EDBMEK_02494;EFOOKO_02539;FHJCBG_02267;FHPENM_01799;FMOEEE_02661;GGEFGC_02543;GHNMBF_02155;GNKNJO_02592;HBKHOP_02195;HFICCC_03514;HGAGGM_02638;HJGKNO_02382;ILJMML_02535;JHLLHD_02047;JPKDEA_02078;KOFDAJ_02495;LPHLDL_02199;MGNIJD_02517;NBILEO_02520;NCJOOM_02764;NJAOBP_03641;NPGDHH_02383;OAHHLH_04862 HK97 family phage major capsid protein
92 group_1090 gene_presence_absence group_1090 group_1090 | SAOUHSC_00181 | none confidence group_1090 hypothetical protein;HK97 gp10 family phage protein SAOUHSC_00181 hypothetical protein none 71.62 1.75 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=71.62; coverage=1.75 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity 198254..199222 matched_representative_sequence=group_10908 AGNJKP_02331;BBHJIH_02175;CKFMFB_01090;DBPPGI_02548;DHHPLE_02172;DPEBLA_01909;EAMBND_02518;EDBMEK_02490;EFOOKO_02543;FHJCBG_02263;FHPENM_01803;FMOEEE_02665;GGEFGC_02547;GHNMBF_02151;GNKNJO_02596;HBKHOP_02191;HFICCC_03510;HGAGGM_02642;HJGKNO_02378;ILJMML_02539;JHLLHD_02043;JPKDEA_02074;KOFDAJ_02491;LPHLDL_02195;MGNIJD_02513;NBILEO_02516;NCJOOM_02760;NJAOBP_03645;NPGDHH_02379;OAHHLH_04858 hypothetical protein
93 group_1014 gene_presence_absence group_1014 group_1014 | SAOUHSC_02916 | none confidence group_1014 Portal protein SAOUHSC_02916 aspartate alpha-decarboxylase none 75.13 5.99 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=75.13; coverage=5.99 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(2682298..2682669) matched_representative_sequence=group_10149 AGNJKP_02337;BBHJIH_02169;CKFMFB_01084;DBPPGI_02554;DHHPLE_02166;DPEBLA_01903;EAMBND_02524;EDBMEK_02496;EFOOKO_02537;FHJCBG_02269;FHPENM_01797;FMOEEE_02659;GGEFGC_02541;GHNMBF_02157;GNKNJO_02590;HBKHOP_02197;HFICCC_03516;HGAGGM_02636;HJGKNO_02384;ILJMML_02533;JHLLHD_02049;JPKDEA_02080;KOFDAJ_02497;LPHLDL_02201;MGNIJD_02519;NBILEO_02522;NCJOOM_02771;NJAOBP_03639;NPGDHH_02385;OAHHLH_04864 aspartate alpha-decarboxylase
94 group_680 gene_presence_absence group_680 group_680 | SAOUHSC_00688 | none confidence group_680 DUF1056 domain-containing protein SAOUHSC_00688 hypothetical protein none 76.19 4.59 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=76.19; coverage=4.59 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(672925..673491) matched_representative_sequence=group_6805 AGNJKP_02338;BBHJIH_02168;CKFMFB_01083;DBPPGI_02555;DHHPLE_02165;DPEBLA_01902;EAMBND_02525;EDBMEK_02497;EFOOKO_02536;FHJCBG_02270;FHPENM_01796;FMOEEE_02658;GGEFGC_02540;GHNMBF_02158;GNKNJO_02589;HBKHOP_02198;HFICCC_03517;HGAGGM_02635;HJGKNO_02385;ILJMML_02532;JHLLHD_02050;JPKDEA_02081;KOFDAJ_02498;LPHLDL_02202;MGNIJD_02520;NBILEO_02523;NCJOOM_02772;NJAOBP_03638;NPGDHH_02386;OAHHLH_04865 hypothetical protein
95 group_6870 gene_presence_absence SAOUHSC_02220-like (group_6870) group_6870 | SAOUHSC_02220 | medium confidence group_6870 Single-stranded DNA-binding protein SAOUHSC_02220 phi ETA orf 18-like protein medium 99.64 63.59 Medium-confidence locus-level GenBank rescue. identity=99.64; coverage=63.59 14 50 0.2800 0 50 0.0000 cases (MRSA) 3.35 40.1233 2.318-694.5 2.31807 694.49 0.000116 12.2619 Panaroo/Bakta+GenBank nucleotide_similarity complement(2065949..2066500) matched_representative_sequence=group_6870 BCINDJ_02231;DBPPGI_02470;DGCAMH_02745;EBFKMK_02745;EFOOKO_02468;GGEFGC_02441;GGOGND_02606;GNKNJO_02371;GNNCOP_01029;HJFIGM_01999;NCJOOM_02790;PBDKDP_02074;PHCLFM_02506;PJCLAL_00875 phi ETA orf 18-like protein
96 group_5172 gene_presence_absence SAOUHSC_00047-like (group_5172) group_5172 | SAOUHSC_00047 | low confidence group_5172 DUF5079 domain-containing protein;hypothetical protein SAOUHSC_00047 hypothetical protein low 96.79 41.67 Low-confidence locus-level GenBank rescue. identity=96.79; coverage=41.67 50 50 1.0000 29 50 0.5800 cases (MRSA) 10.7 73.6102 4.299-1260 4.29877 1260.47 0.000951 12.2237 Panaroo/Bakta+GenBank nucleotide_similarity 49490..50092 matched_representative_sequence=group_5172 AAFANJ_01617;ADDHAP_01059;AGNJKP_00371;BBHJIH_02404;BCINDJ_00967;BGHJOB_01317;BLNHMO_00876;CCGLPJ_01155;CDDCHJ_01698;CIALCM_00191;CJJPLC_00264;CNMMKL_01216;DBPPGI_00773;DGCAMH_01192;DHHPLE_02418;DNJFEH_00881;DPEBLA_02237;EAMBND_02511;EBFKMK_01350;EBHIAF_00748;EDBMEK_00465;EEPHOB_00282;EFOOKO_00491;EOFOFH_01190;FCNEHE_00879;FDFIHM_00939;FHJCBG_01093;FHPENM_00898;FIIBJA_01001;FJPBEI_03077 hypothetical protein
97 set26 gene_presence_absence ;set26 set26 | SAOUHSC_00399 | none confidence ;set26 Superantigen-like protein 11;superantigen-like protein SSL11;hypothetical protein SAOUHSC_00399 superantigen-like protein none 57.54 8.55 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=57.54; coverage=8.55 49 50 0.9800 24 50 0.4800 cases (MRSA) 2.84 35.6939 6.425-198.3 6.42507 198.294 9.39e-05 12.1849 Panaroo/Bakta+GenBank nucleotide_similarity 402508..403185 matched_representative_sequence=set26 AAFANJ_01294;ADDHAP_01159;AGNJKP_00697;BBHJIH_02499;BCINDJ_02664;BGHJOB_02673;CCGLPJ_01480;CDDCHJ_01621;CKFMFB_02202;CNMMKL_02109;DBPPGI_00447;DGCAMH_00867;DHHPLE_02533;DPEBLA_00467;EAMBND_01298;EBFKMK_01025;EBHIAF_02547;EBHIAF_02548;EDBMEK_00791;EEPHOB_02297;EFOOKO_00817;EOFOFH_00863;FCNEHE_01331;FHPENM_00571;FIIBJA_01324;FJPBEI_03080;FMAEJP_02349;FMOEEE_02006;GEIAPO_02221;GGEFGC_00447 superantigen-like protein
98 group_2734 gene_presence_absence group_2734 group_2734 | SAOUHSC_02795 | none confidence group_2734 DUF3784 domain-containing protein SAOUHSC_02795 hypothetical protein none 83.82 12.94 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=83.82; coverage=12.94 49 50 0.9800 24 50 0.4800 cases (MRSA) 2.84 35.6939 6.425-198.3 6.42507 198.294 9.49e-05 12.1803 Panaroo/Bakta+GenBank nucleotide_similarity 2567802..2568110 matched_representative_sequence=group_2734 AAFANJ_01925;ADDHAP_01448;AGNJKP_00079;BBHJIH_01448;BCINDJ_01612;BGHJOB_01949;CCGLPJ_01950;CDDCHJ_00695;CKFMFB_00272;CNMMKL_00616;DBPPGI_01666;DGCAMH_01480;DHHPLE_01446;DPEBLA_01734;EAMBND_02070;EBFKMK_01589;EBHIAF_01815;EDBMEK_01829;EEPHOB_02440;EFOOKO_01934;EOFOFH_01717;FCNEHE_00596;FHJCBG_01356;FHPENM_02456;FIIBJA_01674;FJPBEI_02807;FMAEJP_00809;FMOEEE_01463;GEIAPO_01031;GGEFGC_01635 hypothetical protein
99 sep~~~sea gene_presence_absence ;sep;sea sep~~~sea | SAOUHSC_00009 | none confidence ;sep;sea Enterotoxin type A;staphylococcal enterotoxin type P;staphylococcal enterotoxin type A SAOUHSC_00009 seryl-tRNA synthetase none 34.59 1.66 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=34.59; coverage=1.66 22 50 0.4400 2 50 0.0400 cases (MRSA) 2.84 15.3158 3.83-61.25 3.82955 61.2536 7.08e-06 12.0869 Panaroo/Bakta+GenBank nucleotide_similarity 12786..14072 matched_representative_sequence=sep~~~sea AAFANJ_02743;BCINDJ_02189;DBPPGI_02538;DPEBLA_01919;EDBMEK_02480;EFOOKO_02553;FHPENM_01813;FIIBJA_02009;FJPBEI_01727;FMOEEE_02703;GGEFGC_02557;GHNMBF_02141;GNNCOP_01442;HFCIAM_02326;HFICCC_04023;HJFIGM_02041;HJGKNO_02368;HLEGMA_02301;ILJMML_02549;NJAOBP_03481;NMHDHA_02339;PBDKDP_02032;PHCLFM_02223;PKFOMJ_01696 seryl-tRNA synthetase
100 group_557 gene_presence_absence SAOUHSC_01258 (group_557) group_557 | SAOUHSC_01258 | high confidence group_557 hypothetical protein SAOUHSC_01258 hypothetical protein high 100.00 100.00 High-confidence locus-level GenBank rescue. identity=100.00; coverage=100.00 38 50 0.7600 10 50 0.2000 cases (MRSA) 2.17 11.88 4.68-30.16 4.67992 30.1574 4.49e-06 11.9182 Panaroo/Bakta+GenBank nucleotide_exact_or_contained 1212830..1213657 matched_representative_sequence=group_5575 39_refound_179_pseudo;49_refound_342_pseudo;AAFANJ_02600;AGNJKP_02364;BBHJIH_02141;CNMMKL_00100;DBPPGI_02332;DHHPLE_02138;DPEBLA_01884;EAMBND_02597;EDBMEK_02521;EFOOKO_02379;FCNEHE_02080;FHJCBG_02293;FHPENM_01772;FIIBJA_02046;FJPBEI_01585;FMAEJP_02034;FMOEEE_00557;GEIAPO_02538;GGEFGC_02302;GHNMBF_02183;GNKNJO_02644;HBKHOP_02225;HFCIAM_02363;HFICCC_03943;HGAGGM_02708;HJGKNO_02409;HLEGMA_02338;IGAMFP_02121 hypothetical protein

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08 All significant gene presence/absence hits

Brief interpretation: This section lists all significant gene presence/absence hits at the selected threshold; use it for broader review beyond the top candidates.
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 (MRSA) present case (MRSA) total case (MRSA) frequency control (MSSA) present control (MSSA) total control (MSSA) 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_8632 gene_presence_absence group_8632 group_8632 | SAOUHSC_00003 | none confidence group_8632 hypothetical protein SAOUHSC_00003 hypothetical protein none 42.51 4.17 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=42.51; coverage=4.17 50 50 1.0000 0 50 0.0000 cases (MRSA) 8.8 10201 198.5-5.242e+05 198.519 524185 3.09e-25 40.8265 Panaroo/Bakta+GenBank nucleotide_similarity 3670..3915 matched_representative_sequence=group_8632 AAFANJ_01646;AGNJKP_00338;BBHJIH_02625;BCINDJ_00997;BGHJOB_02138;CCGLPJ_01537;CNMMKL_01926;DBPPGI_01156;DGCAMH_02713;DHHPLE_02450;DPEBLA_02738;EAMBND_00874;EBFKMK_01383;EDBMEK_01615;EFOOKO_01444;FHPENM_01251;FIIBJA_01655;FJPBEI_02140;GGEFGC_01125;GGOGND_00016;GHNMBF_01308;GNKNJO_00279;GNNCOP_02687;HBKHOP_02629;HFCIAM_02218;HFICCC_03024;HGFBEP_01443;HJFIGM_01013;HJGKNO_01151;ILJMML_01475 hypothetical protein
2 group_7349 gene_presence_absence group_7349 group_7349 | SAOUHSC_00014 | none confidence group_7349 MaoC-like domain-containing protein SAOUHSC_00014 hypothetical protein none 40.35 2.33 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=40.35; coverage=2.33 50 50 1.0000 0 50 0.0000 cases (MRSA) 8.8 10201 198.5-5.242e+05 198.519 524185 3.09e-25 40.8265 Panaroo/Bakta+GenBank nucleotide_similarity 17365..18303 matched_representative_sequence=group_7349 AAFANJ_01644;AGNJKP_00340;BBHJIH_02623;BCINDJ_00995;BGHJOB_02140;CCGLPJ_01535;CNMMKL_01928;DBPPGI_01154;DGCAMH_02711;DHHPLE_02448;DPEBLA_02736;EAMBND_00876;EBFKMK_01381;EDBMEK_01617;EFOOKO_01446;FHPENM_01249;FIIBJA_01657;FJPBEI_02138;GGEFGC_01123;GGOGND_00014;GHNMBF_01310;GNKNJO_00277;GNNCOP_02689;HBKHOP_02627;HFCIAM_02220;HFICCC_03022;HGFBEP_01445;HJFIGM_01011;HJGKNO_01153;ILJMML_01473 hypothetical protein
3 group_6207 gene_presence_absence group_6207 group_6207 | SAOUHSC_02467 | none confidence group_6207 GP-PDE domain-containing protein SAOUHSC_02467 alpha-acetolactate decarboxylase none 38.23 2.15 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=38.23; coverage=2.15 50 50 1.0000 0 50 0.0000 cases (MRSA) 8.8 10201 198.5-5.242e+05 198.519 524185 3.09e-25 40.8265 Panaroo/Bakta+GenBank nucleotide_similarity complement(2290323..2291027) matched_representative_sequence=group_6207 AAFANJ_01645;AGNJKP_00339;BBHJIH_02624;BCINDJ_00996;BGHJOB_02139;CCGLPJ_01536;CNMMKL_01927;DBPPGI_01155;DGCAMH_02712;DHHPLE_02449;DPEBLA_02737;EAMBND_00875;EBFKMK_01382;EDBMEK_01616;EFOOKO_01445;FHPENM_01250;FIIBJA_01656;FJPBEI_02139;GGEFGC_01124;GGOGND_00015;GHNMBF_01309;GNKNJO_00278;GNNCOP_02688;HBKHOP_02628;HFCIAM_02219;HFICCC_03023;HGFBEP_01444;HJFIGM_01012;HJGKNO_01152;ILJMML_01474 alpha-acetolactate decarboxylase
4 mecA gene_presence_absence mecA mecA | SAOUHSC_00844 | none confidence mecA PBP2a family beta-lactam-resistant peptidoglycan transpeptidase MecA SAOUHSC_00844 hypothetical protein none 20.93 0.90 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=20.93; coverage=0.90 50 50 1.0000 0 50 0.0000 cases (MRSA) 8.8 10201 198.5-5.242e+05 198.519 524185 3.09e-25 40.8265 Panaroo/Bakta+GenBank nucleotide_similarity 814851..815672 matched_representative_sequence=mecA AAFANJ_01643;AGNJKP_00341;BBHJIH_02622;BCINDJ_00994;BGHJOB_02141;CCGLPJ_01534;CNMMKL_01929;DBPPGI_01153;DGCAMH_02710;DHHPLE_02447;DPEBLA_02735;EAMBND_00877;EBFKMK_01380;EDBMEK_01618;EFOOKO_01447;FHPENM_01248;FIIBJA_01658;FJPBEI_02137;GGEFGC_01122;GGOGND_00013;GHNMBF_01311;GNKNJO_00276;GNNCOP_02690;HBKHOP_02626;HFCIAM_02221;HFICCC_03021;HGFBEP_01446;HJFIGM_01010;HJGKNO_01154;ILJMML_01472 hypothetical protein
5 group_1306 gene_presence_absence ;tnp group_1306 | SAOUHSC_01612 | none confidence ;tnp hypothetical protein;IS6 family IS431R transposase;IS6 family IS431mec transposase SAOUHSC_01612 2-oxoisovalerate dehydrogenase, E1 componentsubunit beta none 37.61 2.52 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=37.61; coverage=2.52 44 50 0.8800 0 50 0.0000 cases (MRSA) 6.16 691.462 37.87-1.262e+04 37.8724 12624.5 1.78e-18 30.1831 Panaroo/Bakta+GenBank nucleotide_similarity complement(1535924..1536907) matched_representative_sequence=49_refound_346 25_refound_104;49_refound_346;59_refound_385_pseudo;60_refound_389_pseudo;70_refound_452_pseudo;85_refound_544_pseudo;89_refound_567_pseudo;90_refound_571;94_refound_594_pseudo;AAFANJ_01647;AGNJKP_00337;BGHJOB_02137;CCGLPJ_01538;CNMMKL_01930;DBPPGI_01157;DHHPLE_02451;EAMBND_00873;EBFKMK_01384;EDBMEK_01614;EFOOKO_01443;FHPENM_01252;FIIBJA_01654;FJPBEI_02141;GGEFGC_01126;GGOGND_00017;GHNMBF_01307;GNKNJO_00280;GNNCOP_02691;HFCIAM_02217;HFICCC_04308 2-oxoisovalerate dehydrogenase, E1 componentsubunit beta
6 group_5731 gene_presence_absence group_5731 group_5731 | SAOUHSC_00469 | none confidence group_5731 hypothetical protein;Phage protein SAOUHSC_00469 regulatory protein SpoVG none 34.34 16.13 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=34.34; coverage=16.13 46 50 0.9200 5 50 0.1000 cases (MRSA) 6.21 85.4848 23.04-317.2 23.0382 317.198 1.5e-19 28.2415 Panaroo/Bakta+GenBank nucleotide_similarity 468929..469231 matched_representative_sequence=group_5731 AAFANJ_01637;AGNJKP_00347;BBHJIH_02611;BCINDJ_00988;BGHJOB_02147;CCGLPJ_01523;CJHDKP_02388;CLDKNN_00890;DBPPGI_01147;DGCAMH_02699;DHHPLE_02436;DPEBLA_02459;EAMBND_02662;EBFKMK_01369;EDBMEK_01624;EFOOKO_01453;FFPFOI_02215;FHPENM_01242;FIIBJA_01664;FJPBEI_02126;FMNEAL_02262;GGEFGC_01116;GGOGND_00007;GHNMBF_01317;GNKNJO_00270;GNNCOP_02700;HBKHOP_02615;HFCIAM_02227;HFICCC_03015;HGFBEP_01452 regulatory protein SpoVG
7 group_5706 gene_presence_absence group_5706 group_5706 | SAOUHSC_00753 | none confidence group_5706 Pyridoxal phosphate-dependent enzyme;hypothetical protein SAOUHSC_00753 hypothetical protein none 22.38 5.13 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=22.38; coverage=5.13 46 50 0.9200 5 50 0.1000 cases (MRSA) 6.21 85.4848 23.04-317.2 23.0382 317.198 1.5e-19 28.2415 Panaroo/Bakta+GenBank nucleotide_similarity complement(736562..737080) matched_representative_sequence=group_5706 AAFANJ_01638;AGNJKP_00346;BBHJIH_02610;BCINDJ_00989;BGHJOB_02146;CCGLPJ_01522;CJHDKP_02389;CLDKNN_00891;DBPPGI_01148;DGCAMH_02698;DHHPLE_02435;DPEBLA_02460;EAMBND_02661;EBFKMK_01368;EDBMEK_01623;EFOOKO_01452;FFPFOI_02216;FHPENM_01243;FIIBJA_01663;FJPBEI_02125;FMNEAL_02261;GGEFGC_01117;GGOGND_00008;GHNMBF_01316;GNKNJO_00271;GNNCOP_02701;HBKHOP_02614;HFCIAM_02226;HFICCC_03016;HGFBEP_01451 hypothetical protein
8 group_5704 gene_presence_absence group_5704 group_5704 | SAOUHSC_00027 | none confidence group_5704 Transposase;DUF1643 domain-containing protein SAOUHSC_00027 23S rRNA(pseudouridine(1915)-N(3))-methyltransferase RlmH none 42.35 1.78 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=42.35; coverage=1.78 46 50 0.9200 5 50 0.1000 cases (MRSA) 6.21 85.4848 23.04-317.2 23.0382 317.198 1.5e-19 28.2415 Panaroo/Bakta+GenBank nucleotide_similarity 33691..34170 matched_representative_sequence=group_5704 AAFANJ_01639;AGNJKP_00345;BBHJIH_02609;BCINDJ_00990;BGHJOB_02145;CCGLPJ_01521;CJHDKP_02390;CLDKNN_00892;DBPPGI_01149;DGCAMH_02697;DHHPLE_02434;DPEBLA_02461;EAMBND_02660;EBFKMK_01367;EDBMEK_01622;EFOOKO_01451;FFPFOI_02217;FHPENM_01244;FIIBJA_01662;FJPBEI_02124;FMNEAL_02260;GGEFGC_01118;GGOGND_00009;GHNMBF_01315;GNKNJO_00272;GNNCOP_02702;HBKHOP_02613;HFCIAM_02225;HFICCC_03017;HGFBEP_01450 23S rRNA(pseudouridine(1915)-N(3))-methyltransferase RlmH
9 group_4661 gene_presence_absence group_4661 group_4661 | SAOUHSC_03000 | none confidence group_4661 hypothetical protein;Transposon tn552 dna-invertase binr SAOUHSC_03000 capsular polysaccharide biosynthesis proteinCapA none 20.59 0.98 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=20.59; coverage=0.98 31 50 0.6200 0 50 0.0000 cases (MRSA) 6.05 163.154 9.511-2799 9.5112 2798.72 1.51e-12 22.1711 Panaroo/Bakta+GenBank nucleotide_similarity complement(2772939..2773601) matched_representative_sequence=group_4661 AAFANJ_01635;AGNJKP_00349;BCINDJ_00986;BGHJOB_02149;DBPPGI_01145;DPEBLA_02456;DPEBLA_02457;EAMBND_02664;EDBMEK_01626;EFOOKO_01455;FHPENM_01240;FIIBJA_01666;GGEFGC_01114;GGOGND_00005;GHNMBF_01319;GNKNJO_00268;HFCIAM_02229;HFICCC_03013;HGFBEP_01454;HJFIGM_01002;HJGKNO_01162;ILJMML_01464;KOFDAJ_02645;NBILEO_02656;NCJOOM_00377;NJAOBP_03670;NKBKLH_01902;NMHDHA_01202;PBDKDP_00805;PHCLFM_01334 capsular polysaccharide biosynthesis proteinCapA
10 group_4071 gene_presence_absence group_4071 group_4071 | SAOUHSC_01015 | none confidence group_4071 DUF927 domain-containing protein SAOUHSC_01015 phosphoribosylaminoimidazole synthetase none 21.40 0.89 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=21.40; coverage=0.89 31 50 0.6200 0 50 0.0000 cases (MRSA) 6.05 163.154 9.511-2799 9.5112 2798.72 1.51e-12 22.1711 Panaroo/Bakta+GenBank nucleotide_similarity 986197..987225 matched_representative_sequence=group_4071 AAFANJ_01633;AGNJKP_00351;BCINDJ_00984;BGHJOB_02151;DBPPGI_01143;DPEBLA_02454;EAMBND_02667;EDBMEK_01628;EFOOKO_01457;FHPENM_01238;FIIBJA_01668;GGEFGC_01112;GGOGND_00003;GHNMBF_01321;GNKNJO_00266;HFCIAM_02231;HFICCC_03011;HGFBEP_01456;HJFIGM_01000;HJGKNO_01164;ILJMML_01462;KOFDAJ_02643;NBILEO_02654;NCJOOM_00375;NJAOBP_03668;NKBKLH_01900;NMHDHA_01200;PBDKDP_00803;PHCLFM_01336;PKCIIG_00851 phosphoribosylaminoimidazole synthetase
11 mecR1 gene_presence_absence mecR1 mecR1 | SAOUHSC_00005 | none confidence mecR1 beta-lactam sensor/signal transducer MecR1 SAOUHSC_00005 DNA gyrase subunit B none 34.09 1.11 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=34.09; coverage=1.11 31 50 0.6200 0 50 0.0000 cases (MRSA) 6.05 163.154 9.511-2799 9.5112 2798.72 1.62e-12 22.1406 Panaroo/Bakta+GenBank nucleotide_similarity 5034..6968 matched_representative_sequence=mecR1 AAFANJ_01642;AGNJKP_00342;BCINDJ_00993;BGHJOB_02142;DBPPGI_01152;EAMBND_00878;EDBMEK_01619;EFOOKO_01448;FHPENM_01247;FIIBJA_01659;GGEFGC_01121;GGOGND_00012;GHNMBF_01312;GNKNJO_00275;HFCIAM_02222;HFICCC_03020;HGFBEP_01447;HJFIGM_01009;HJGKNO_01155;ILJMML_01471;KOFDAJ_01933;MGNIJD_00584;NBILEO_01984;NCJOOM_00384;NJAOBP_03677;NKBKLH_01909;NMHDHA_01209;PBDKDP_00812;PHCLFM_01327;PKCIIG_00861 DNA gyrase subunit B
12 group_5724 gene_presence_absence group_5724 group_5724 | SAOUHSC_02801 | none confidence group_5724 UTP-glucose-1-phosphate uridylyltransferase SAOUHSC_02801 UTP-glucose-1-phosphate uridylyltransferase none 33.43 1.27 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=33.43; coverage=1.27 29 50 0.5800 0 50 0.0000 cases (MRSA) 6.16 138.581 8.093-2373 8.09304 2373 7.52e-12 21.2384 Panaroo/Bakta+GenBank nucleotide_similarity complement(2576833..2577615) matched_representative_sequence=group_5724 AAFANJ_01649;AGNJKP_00335;BGHJOB_02136;DBPPGI_01159;DPEBLA_02444;EAMBND_00870;EAMBND_00871;EDBMEK_01612;EFOOKO_01441;FHPENM_01254;FIIBJA_01652;GGEFGC_01128;GGOGND_00019;GHNMBF_01305;GNKNJO_00282;GNKNJO_00283;HFCIAM_02215;HFICCC_04118;HGFBEP_01437;HJGKNO_01148;ILJMML_01478;KOFDAJ_01925;KOFDAJ_01926;MGNIJD_01845;NBILEO_01976;NBILEO_01977;NCJOOM_00391;NCJOOM_00392;NJAOBP_05133;NKBKLH_01915 UTP-glucose-1-phosphate uridylyltransferase
13 group_4347 gene_presence_absence recA; group_4347 | SAOUHSC_01716 | none confidence recA; Recombinase RecA;hypothetical protein SAOUHSC_01716 hypothetical protein none 19.09 1.11 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=19.09; coverage=1.11 27 50 0.5400 0 50 0.0000 cases (MRSA) 5.81 118.191 6.909-2022 6.90926 2021.81 7.89e-11 19.9879 Panaroo/Bakta+GenBank nucleotide_similarity complement(1621052..1622320) matched_representative_sequence=group_4347 AAFANJ_01634;AGNJKP_00350;BGHJOB_02150;DBPPGI_01144;DPEBLA_02455;EAMBND_02665;EAMBND_02666;EDBMEK_01627;EFOOKO_01456;FHPENM_01239;FIIBJA_01667;GGEFGC_01113;GGOGND_00004;GHNMBF_01320;GNKNJO_00267;HFCIAM_02230;HFICCC_03012;HGFBEP_01455;HJGKNO_01163;ILJMML_01463;KOFDAJ_02644;NBILEO_02655;NJAOBP_03669;NKBKLH_01901;NMHDHA_01201;PHCLFM_01335;PKCIIG_00852;PKFOMJ_01317 hypothetical protein
14 group_5720 gene_presence_absence rplI group_5720 | SAOUHSC_00017 | none confidence rplI hypothetical protein;Type I restriction-modification system restriction subunit R SAOUHSC_00017 rplI 50S ribosomal protein L9 none 35.01 3.45 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=35.01; coverage=3.45 31 50 0.6200 2 50 0.0400 cases (MRSA) 6.05 31.3385 7.798-125.9 7.79804 125.942 1.55e-12 19.7795 Panaroo/Bakta+GenBank nucleotide_similarity 20282..20734 matched_representative_sequence=group_5720 AAFANJ_01641;AGNJKP_00343;BCINDJ_00992;BGHJOB_02143;CPFPLH_01651;CPMMBP_01651;DBPPGI_01151;EAMBND_00879;EDBMEK_01620;EFOOKO_01449;FHPENM_01246;FIIBJA_01660;GGEFGC_01120;GGOGND_00011;GHNMBF_01313;GNKNJO_00274;HFCIAM_02223;HFICCC_03019;HGFBEP_01448;HJFIGM_01008;HJGKNO_01156;ILJMML_01470;KOFDAJ_01934;MGNIJD_00585;NBILEO_01985;NCJOOM_00383;NJAOBP_03676;NKBKLH_01908;NMHDHA_01208;PBDKDP_00811 50S ribosomal protein L9
15 group_5764 gene_presence_absence group_5764 group_5764 | SAOUHSC_01154 | none confidence group_5764 hypothetical protein SAOUHSC_01154 hypothetical protein none 38.47 4.27 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=38.47; coverage=4.27 32 50 0.6400 5 50 0.1000 cases (MRSA) 6.42 14.5332 5.071-41.65 5.07059 41.6546 4.46e-13 19.2119 Panaroo/Bakta+GenBank nucleotide_similarity 1104514..1105077 matched_representative_sequence=group_5764 AAFANJ_01636;AGNJKP_00348;BCINDJ_00987;BGHJOB_02148;CJHDKP_02387;CLDKNN_00889;DBPPGI_01146;DPEBLA_02458;EAMBND_02663;EDBMEK_01625;EFOOKO_01454;FFPFOI_02214;FHPENM_01241;FIIBJA_01665;FMNEAL_02263;GGEFGC_01115;GGOGND_00006;GHNMBF_01318;GNKNJO_00269;HFCIAM_02228;HFICCC_03014;HGFBEP_01453;HJFIGM_01003;HJGKNO_01161;ILJMML_01465;JFACDE_02170;KOFDAJ_02646;MGNIJD_00590;NBILEO_02657;NCJOOM_00378 hypothetical protein
16 group_8214 gene_presence_absence group_8214 group_8214 | SAOUHSC_02176 | none confidence group_8214 hypothetical protein SAOUHSC_02176 hypothetical protein none 38.37 6.25 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=38.37; coverage=6.25 25 50 0.5000 0 50 0.0000 cases (MRSA) 5.4 101 5.906-1727 5.90622 1727.16 9e-10 18.7040 Panaroo/Bakta+GenBank nucleotide_similarity complement(2037590..2037766) matched_representative_sequence=group_8214 AAFANJ_01648;AGNJKP_00336;DBPPGI_01158;EAMBND_00872;EDBMEK_01613;EFOOKO_01442;FHPENM_01253;FIIBJA_01653;GGEFGC_01127;GGOGND_00018;GHNMBF_01306;GNKNJO_00281;HFCIAM_02216;HFICCC_04119;HGFBEP_01441;HJGKNO_01149;ILJMML_01477;KOFDAJ_01927;MGNIJD_01846;NBILEO_01978;NCJOOM_00390;NJAOBP_05134;NMHDHA_01215;PHCLFM_01321;PKFOMJ_01331 hypothetical protein
17 group_8016 gene_presence_absence group_8016 group_8016 | SAOUHSC_00037 | none confidence group_8016 hypothetical protein SAOUHSC_00037 hypothetical protein none 19.93 5.15 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=19.93; coverage=5.15 23 50 0.4600 0 50 0.0000 cases (MRSA) 5.24 86.3091 5.045-1476 5.04547 1476.42 4.78e-09 17.7520 Panaroo/Bakta+GenBank nucleotide_similarity 40821..42014 matched_representative_sequence=group_8016 AAFANJ_01632;BGHJOB_02152;DBPPGI_01142;EAMBND_02668;EDBMEK_01629;EFOOKO_01458;FHPENM_01237;FIIBJA_01669;GGEFGC_01111;GGOGND_00002;GHNMBF_01322;GNKNJO_00265;HFCIAM_02232;HFICCC_03010;HJGKNO_01165;ILJMML_01461;KOFDAJ_02642;NBILEO_02653;NJAOBP_03667;NKBKLH_01899;NMHDHA_01199;PHCLFM_01337;PKFOMJ_01315 hypothetical protein
18 group_7603 gene_presence_absence rplP group_7603 | SAOUHSC_02505 | none confidence rplP 5-methylcytosine-specific restriction enzyme a SAOUHSC_02505 rplP 50S ribosomal protein L16 none 37.92 4.57 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=37.92; coverage=4.57 23 50 0.4600 0 50 0.0000 cases (MRSA) 5.24 86.3091 5.045-1476 5.04547 1476.42 4.78e-09 17.7520 Panaroo/Bakta+GenBank nucleotide_similarity complement(2313509..2313943) matched_representative_sequence=group_7603 AAFANJ_01628;BGHJOB_01267;DBPPGI_00788;EAMBND_02491;EDBMEK_00450;EFOOKO_00476;FHPENM_00913;FIIBJA_00989;GGEFGC_02528;GGOGND_02602;GHNMBF_02580;GNKNJO_02552;HFCIAM_01255;HFICCC_03006;HJGKNO_00519;ILJMML_00862;KOFDAJ_02546;NBILEO_02571;NJAOBP_04407;NKBKLH_01240;NMHDHA_02596;PHCLFM_00408;PKFOMJ_01311 50S ribosomal protein L16
19 group_6616 gene_presence_absence group_6616 group_6616 | SAOUHSC_00942 | none confidence group_6616 Restriction endonuclease SAOUHSC_00942 GTP pyrophosphokinase none 43.75 2.58 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=43.75; coverage=2.58 23 50 0.4600 0 50 0.0000 cases (MRSA) 5.24 86.3091 5.045-1476 5.04547 1476.42 4.78e-09 17.7520 Panaroo/Bakta+GenBank nucleotide_similarity 914181..914816 matched_representative_sequence=group_6616 AAFANJ_01627;BGHJOB_01268;DBPPGI_00787;EAMBND_02492;EDBMEK_00451;EFOOKO_00477;FHPENM_00912;FIIBJA_00990;GGEFGC_02527;GGOGND_02601;GHNMBF_02581;GNKNJO_02551;HFCIAM_01256;HFICCC_03005;HJGKNO_00520;ILJMML_00861;KOFDAJ_02545;NBILEO_02570;NJAOBP_04406;NKBKLH_01239;NMHDHA_02595;PHCLFM_00409;PKFOMJ_01310 GTP pyrophosphokinase
20 group_2737 gene_presence_absence group_2737 group_2737 | SAOUHSC_00036 | none confidence group_2737 Metallo-beta-lactamase domain-containing protein SAOUHSC_00036 hypothetical protein none 63.08 2.09 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=63.08; coverage=2.09 23 50 0.4600 0 50 0.0000 cases (MRSA) 5.24 86.3091 5.045-1476 5.04547 1476.42 4.78e-09 17.7520 Panaroo/Bakta+GenBank nucleotide_similarity 39468..40802 matched_representative_sequence=group_2737 AAFANJ_01629;BGHJOB_01266;DBPPGI_00789;EAMBND_02490;EDBMEK_00449;EFOOKO_00475;FHPENM_00914;FIIBJA_00988;GGEFGC_02529;GGOGND_02603;GHNMBF_02579;GNKNJO_02553;HFCIAM_01254;HFICCC_03007;HJGKNO_00518;ILJMML_00863;KOFDAJ_02547;NBILEO_02572;NJAOBP_04409;NKBKLH_01241;NMHDHA_02597;PHCLFM_00407;PKFOMJ_01312 hypothetical protein
21 group_2330 gene_presence_absence group_2330 group_2330 | SAOUHSC_00932 | none confidence group_2330 ACP synthase SAOUHSC_00932 oligopeptide ABC transporter permease none 30.23 1.52 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=30.23; coverage=1.52 23 50 0.4600 0 50 0.0000 cases (MRSA) 5.24 86.3091 5.045-1476 5.04547 1476.42 4.78e-09 17.7520 Panaroo/Bakta+GenBank nucleotide_similarity 904625..905506 matched_representative_sequence=group_2330 AAFANJ_01631;BGHJOB_02153;DBPPGI_01141;EAMBND_02669;EDBMEK_01630;EFOOKO_01459;FHPENM_01236;FIIBJA_01670;GGEFGC_01110;GGOGND_00001;GHNMBF_01323;GNKNJO_00264;HFCIAM_02233;HFICCC_03009;HJGKNO_01166;ILJMML_01460;KOFDAJ_02641;NBILEO_02652;NJAOBP_03666;NKBKLH_01898;NMHDHA_01198;PHCLFM_01338;PKFOMJ_01314 oligopeptide ABC transporter permease
22 group_470 gene_presence_absence group_470 group_470 | SAOUHSC_02667 | none confidence group_470 Transcriptional regulator SAOUHSC_02667 hypothetical protein none 91.39 6.26 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=91.39; coverage=6.26 23 50 0.4600 0 50 0.0000 cases (MRSA) 5.24 86.3091 5.045-1476 5.04547 1476.42 4.78e-09 17.7520 Panaroo/Bakta+GenBank nucleotide_similarity complement(2452049..2453326) matched_representative_sequence=group_4707 AAFANJ_01630;BGHJOB_01265;DBPPGI_00790;EAMBND_02489;EDBMEK_00448;EFOOKO_00474;FHPENM_00915;FIIBJA_00987;GGEFGC_02530;GGOGND_02604;GHNMBF_02578;GNKNJO_02554;HFCIAM_01253;HFICCC_03008;HJGKNO_00517;ILJMML_00864;KOFDAJ_02548;NBILEO_02573;NJAOBP_04410;NKBKLH_01242;NMHDHA_02598;PHCLFM_00406;PKFOMJ_01313 hypothetical protein
23 fusC gene_presence_absence fusC fusC | SAOUHSC_00881 | none confidence fusC fusidic acid resistance EF-G-binding protein FusC SAOUHSC_00881 hypothetical protein none 35.50 2.50 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=35.50; coverage=2.50 25 50 0.5000 0 50 0.0000 cases (MRSA) 4.37 101 5.906-1727 5.90622 1727.16 2.98e-08 17.1840 Panaroo/Bakta+GenBank nucleotide_similarity 846360..846734 matched_representative_sequence=fusC AAFANJ_01671;BBHJIH_02392;BCINDJ_00977;CCGLPJ_01142;CNMMKL_01942;DGCAMH_01205;DHHPLE_02430;DPEBLA_02448;EBFKMK_01363;FIIBJA_01630;HBKHOP_02435;HJFIGM_00994;JHLLHD_02319;JPKDEA_02390;KBDKBJ_02551;LPHLDL_02437;NCJOOM_00369;NNICCC_00250;NPGDHH_01376;OAHHLH_06628;OMNKFL_02464;PBDKDP_00797;PJCLAL_01208;PKCIIG_00845;PKFOMJ_01354 hypothetical protein
24 group_908 gene_presence_absence group_908 group_908 | SAOUHSC_01228 | none confidence group_908 DUF771 domain-containing protein;hypothetical protein SAOUHSC_01228 transcriptional repressor CodY none 65.63 4.26 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=65.63; coverage=4.26 25 50 0.5000 0 50 0.0000 cases (MRSA) 4.37 101 5.906-1727 5.90622 1727.16 2.98e-08 17.1840 Panaroo/Bakta+GenBank nucleotide_similarity 1179705..1180478 matched_representative_sequence=group_9085 AAFANJ_01672;BBHJIH_02391;BCINDJ_00978;CCGLPJ_01141;CNMMKL_01943;DGCAMH_01206;DHHPLE_02431;DPEBLA_02449;EBFKMK_01364;FIIBJA_01629;HBKHOP_02436;HJFIGM_00995;JHLLHD_02320;JPKDEA_02389;KBDKBJ_02550;LPHLDL_02438;NCJOOM_00370;NNICCC_00249;NPGDHH_01375;OAHHLH_06627;OMNKFL_02463;PBDKDP_00798;PJCLAL_01207;PKCIIG_00846;PKFOMJ_01355 transcriptional repressor CodY
25 group_1790 gene_presence_absence yoeB; group_1790 | SAOUHSC_02756 | none confidence yoeB; Putative mRNA interferase YoeB;Txe/YoeB family addiction module toxin SAOUHSC_02756 hypothetical protein none 95.51 18.35 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=95.51; coverage=18.35 46 50 0.9200 13 50 0.2600 cases (MRSA) 3.09 28.7037 9.085-90.68 9.08545 90.6837 3.2e-08 15.3380 Panaroo/Bakta+GenBank nucleotide_similarity complement(2534034..2534300) matched_representative_sequence=group_1790 AAFANJ_01964;AGNJKP_00048;BBHJIH_01486;BCINDJ_01652;BGHJOB_01913;CCGLPJ_01988;CKFMFB_00238;CNMMKL_00582;DBPPGI_01705;DGCAMH_01518;DHHPLE_01484;DPEBLA_01700;EAMBND_01061;EBFKMK_01627;EBHIAF_01777;EDBMEK_01868;EEPHOB_01301;EFOOKO_01973;EOFOFH_01680;FHPENM_02417;FIIBJA_01713;FJPBEI_01205;FMOEEE_01426;GGEFGC_01674;GGOGND_00304;GHNMBF_01989;GNFCHG_01431;GNKNJO_01007;GNNCOP_01677;HBKHOP_01496 hypothetical protein
26 group_5705 gene_presence_absence group_5705 group_5705 | SAOUHSC_01005 | none confidence group_5705 ISSau3 transposase;Transposase SAOUHSC_01005 hypothetical protein none 19.76 0.92 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=19.76; coverage=0.92 28 50 0.5600 2 50 0.0400 cases (MRSA) 3.48 24.5733 6.144-98.28 6.14429 98.278 3.04e-08 15.1361 Panaroo/Bakta+GenBank nucleotide_similarity complement(977138..977455) matched_representative_sequence=group_5705 AAFANJ_01640;AGNJKP_00344;BCINDJ_00991;BGHJOB_02144;DBPPGI_01150;EDBMEK_01621;EFOOKO_01450;FHPENM_01245;FIIBJA_01661;GGEFGC_01119;GGOGND_00010;GHNMBF_01314;GNKNJO_00273;HFCIAM_02224;HFICCC_03018;HGAGGM_00189;HGFBEP_01449;HJFIGM_01007;HJGKNO_01157;IGAMFP_01293;ILJMML_01469;MGNIJD_00586;NCJOOM_00382;NJAOBP_03675;NKBKLH_01907;NMHDHA_01207;PBDKDP_00810;PHCLFM_01329;PKCIIG_00858;PKFOMJ_01323 hypothetical protein
27 group_3186 gene_presence_absence dnaD; group_3186 | SAOUHSC_00017 | none confidence dnaD; DnaD domain-containing protein;hypothetical protein;DnaD domain protein SAOUHSC_00017 rplI 50S ribosomal protein L9 none 35.34 1.01 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=35.34; coverage=1.01 39 50 0.7800 7 50 0.1400 cases (MRSA) 2.76 19.9217 7.214-55.01 7.21397 55.0149 2.08e-08 14.9982 Panaroo/Bakta+GenBank nucleotide_similarity 20282..20734 matched_representative_sequence=group_3186 AAFANJ_02595;AGNJKP_02359;BBHJIH_02146;BGHJOB_02221;CNMMKL_00105;DBPPGI_02327;DHHPLE_02143;DPEBLA_01889;EAMBND_02602;EDBMEK_02516;EFOOKO_02384;FCNEHE_02085;FHJCBG_02287;FHPENM_01777;FIIBJA_02041;FMOEEE_00552;GGEFGC_02297;GGOGND_02255;GHNMBF_02177;GNKNJO_02639;HBKHOP_02220;HFCIAM_02358;HFICCC_03938;HGAGGM_02617;HJGKNO_02404;HLEGMA_02333;IGAMFP_02126;ILJMML_02513;JHLLHD_02072;JPKDEA_02103 50S ribosomal protein L9
28 group_5259 gene_presence_absence group_5259 group_5259 | SAOUHSC_00404 | none confidence group_5259 Uncharacterized lipoprotein SA0399;Uncharacterized lipoprotein SAB0394;Uncharacterized lipoprotein SAOUHSC_00404;Csa1 family protein;hypothetical protein SAOUHSC_00404 hypothetical protein none 63.66 6.27 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=63.66; coverage=6.27 37 50 0.7400 7 50 0.1400 cases (MRSA) 3.13 16.1111 5.964-43.52 5.96413 43.5215 6.56e-08 14.1931 Panaroo/Bakta+GenBank nucleotide_similarity 406302..407087 matched_representative_sequence=group_5259 AAFANJ_01291;BBHJIH_02505;BCINDJ_02669;CNMMKL_02113;DBPPGI_00444;DHHPLE_02539;EAMBND_01305;EBHIAF_02542;EDBMEK_00794;EEPHOB_02302;EEPHOB_02303;EFOOKO_00820;FCNEHE_01319;FHPENM_00568;FIIBJA_01327;FJPBEI_01017;FMOEEE_02003;GGEFGC_00444;GGOGND_00831;GHNMBF_00489;GNKNJO_01069;GNNCOP_00040;HBKHOP_02508;HFCIAM_01594;HFICCC_04060;HGAGGM_01666;HGFBEP_02075;HJFIGM_02553;HJGKNO_00864;HLEGMA_01304 hypothetical protein
29 group_7350 gene_presence_absence group_7350 group_7350 | SAOUHSC_02564 | none confidence group_7350 Glyoxalase/fosfomycin resistance/dioxygenase domain-containing protein SAOUHSC_02564 urease accessory protein UreG none 36.21 3.73 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=36.21; coverage=3.73 19 50 0.3800 0 50 0.0000 cases (MRSA) 3.73 62.5238 3.645-1073 3.64488 1072.52 6.88e-06 14.1287 Panaroo/Bakta+GenBank nucleotide_similarity 2355860..2356474 matched_representative_sequence=group_7350 BBHJIH_02620;CCGLPJ_01532;CNMMKL_01924;DGCAMH_02708;DHHPLE_02445;DPEBLA_02746;EBFKMK_01378;FJPBEI_02135;GNNCOP_02692;HBKHOP_02624;JHLLHD_02651;JPKDEA_02622;KBDKBJ_02756;LPHLDL_02452;NNICCC_00267;NPGDHH_02733;OAHHLH_06612;OMNKFL_02691;PJCLAL_02764 urease accessory protein UreG
30 group_3788 gene_presence_absence group_3788 group_3788 | SAOUHSC_00598 | none confidence group_3788 Transcriptional regulator SAOUHSC_00598 hypothetical protein none 28.00 1.72 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=28.00; coverage=1.72 19 50 0.3800 0 50 0.0000 cases (MRSA) 3.73 62.5238 3.645-1073 3.64488 1072.52 6.88e-06 14.1287 Panaroo/Bakta+GenBank nucleotide_similarity 593183..593752 matched_representative_sequence=group_3788 BBHJIH_02619;CCGLPJ_01531;CNMMKL_01923;DGCAMH_02707;DHHPLE_02444;DPEBLA_02747;EBFKMK_01377;FJPBEI_02134;GNNCOP_02693;HBKHOP_02623;JHLLHD_02650;JPKDEA_02621;KBDKBJ_02755;LPHLDL_02451;NNICCC_00268;NPGDHH_02732;OAHHLH_06613;OMNKFL_02690;PJCLAL_02763 hypothetical protein
31 spn gene_presence_absence SAOUHSC_00401-like (spn) spn | SAOUHSC_00401 | low confidence spn myeloperoxidase inhibitor SPIN SAOUHSC_00401 hypothetical protein low 99.35 49.19 Low-confidence locus-level GenBank rescue. identity=99.35; coverage=49.19 50 50 1.0000 29 50 0.5800 cases (MRSA) 37.1 73.6102 4.299-1260 4.29877 1260.47 2.13e-05 13.8735 Panaroo/Bakta+GenBank nucleotide_similarity complement(404819..405127) matched_representative_sequence=25_refound_103 0_refound_3;25_refound_103;30_refound_135;46_refound_294;56_refound_368;57_refound_378;61_refound_395;65_refound_430;67_refound_440;69_refound_446;72_refound_462;78_refound_506;79_refound_511;83_refound_527;91_refound_573;93_refound_586;96_refound_605;98_refound_617;99_refound_621;AGNJKP_00699;BBHJIH_02502;BCINDJ_02666;BGHJOB_02675;BLNHMO_01869;CCGLPJ_01482;CDDCHJ_01623;CIALCM_01878;CJJPLC_01922;CKFMFB_02200;DGCAMH_00865 hypothetical protein
32 group_7923 gene_presence_absence groES group_7923 | SAOUHSC_02255 | none confidence groES Pyridoxal phosphate-dependent enzyme SAOUHSC_02255 groES co-chaperonin GroES none 33.50 4.81 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=33.50; coverage=4.81 18 50 0.3600 0 50 0.0000 cases (MRSA) 3.63 57.4923 3.348-987.4 3.3475 987.412 1.48e-05 13.6750 Panaroo/Bakta+GenBank nucleotide_similarity complement(2088452..2088736) matched_representative_sequence=group_7923 BBHJIH_02592;CCGLPJ_01540;CNMMKL_01932;DGCAMH_01210;DHHPLE_02453;DPEBLA_01173;EBFKMK_01386;GNNCOP_01027;HBKHOP_02595;JHLLHD_02602;JPKDEA_02608;KBDKBJ_02559;LPHLDL_02460;NNICCC_00259;NPGDHH_01385;OAHHLH_06604;OMNKFL_02678;PJCLAL_02185 co-chaperonin GroES
33 group_7771 gene_presence_absence group_7771 group_7771 | SAOUHSC_02331 | none confidence group_7771 Phage protein SAOUHSC_02331 hypothetical protein none 7.58 4.42 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=7.58; coverage=4.42 18 50 0.3600 0 50 0.0000 cases (MRSA) 3.63 57.4923 3.348-987.4 3.3475 987.412 1.48e-05 13.6750 Panaroo/Bakta+GenBank nucleotide_similarity complement(2161547..2162236) matched_representative_sequence=group_7771 BBHJIH_02593;CCGLPJ_01541;CNMMKL_01934;DGCAMH_01211;DHHPLE_02454;DPEBLA_01172;EBFKMK_01387;GNNCOP_01026;HBKHOP_02596;JHLLHD_02603;JPKDEA_02607;KBDKBJ_02558;LPHLDL_02461;NNICCC_00258;NPGDHH_01383;OAHHLH_06602;OMNKFL_02677;PJCLAL_02184 hypothetical protein
34 group_7016 gene_presence_absence group_7016 group_7016 | SAOUHSC_01949 | none confidence group_7016 Transposase SAOUHSC_01949 intracellular serine protease none 25.52 3.16 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=25.52; coverage=3.16 18 50 0.3600 0 50 0.0000 cases (MRSA) 3.63 57.4923 3.348-987.4 3.3475 987.412 1.48e-05 13.6750 Panaroo/Bakta+GenBank nucleotide_similarity complement(1851533..1852906) matched_representative_sequence=group_7016 BBHJIH_02591;CCGLPJ_01539;CNMMKL_01931;DGCAMH_01209;DHHPLE_02452;DPEBLA_01174;EBFKMK_01385;GNNCOP_01028;HBKHOP_02594;JHLLHD_02601;JPKDEA_02609;KBDKBJ_02560;LPHLDL_02459;NNICCC_00260;NPGDHH_01386;OAHHLH_06605;OMNKFL_02679;PJCLAL_02186 intracellular serine protease
35 group_5287 gene_presence_absence group_5287 group_5287 | SAOUHSC_00027 | none confidence group_5287 DNA-directed DNA polymerase family A palm domain-containing protein SAOUHSC_00027 23S rRNA(pseudouridine(1915)-N(3))-methyltransferase RlmH none 35.29 0.91 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=35.29; coverage=0.91 18 50 0.3600 0 50 0.0000 cases (MRSA) 3.63 57.4923 3.348-987.4 3.3475 987.412 1.48e-05 13.6750 Panaroo/Bakta+GenBank nucleotide_similarity 33691..34170 matched_representative_sequence=group_5287 BBHJIH_02598;CCGLPJ_01546;CNMMKL_01938;DGCAMH_01216;DHHPLE_02459;DPEBLA_01168;EBFKMK_01392;GNNCOP_01021;HBKHOP_02601;JHLLHD_02608;JPKDEA_02602;KBDKBJ_02554;LPHLDL_02466;NNICCC_00254;NPGDHH_01379;OAHHLH_06597;OMNKFL_02672;PJCLAL_02179 23S rRNA(pseudouridine(1915)-N(3))-methyltransferase RlmH
36 group_5286 gene_presence_absence group_5286 group_5286 | SAOUHSC_03002 | none confidence group_5286 N-glycosyltransferase SAOUHSC_03002 N-glycosyltransferase none 25.45 4.30 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=25.45; coverage=4.30 18 50 0.3600 0 50 0.0000 cases (MRSA) 3.63 57.4923 3.348-987.4 3.3475 987.412 1.48e-05 13.6750 Panaroo/Bakta+GenBank nucleotide_similarity 2775174..2776412 matched_representative_sequence=group_5286 BBHJIH_02597;CCGLPJ_01545;CNMMKL_01937;DGCAMH_01215;DHHPLE_02458;DPEBLA_01169;EBFKMK_01391;GNNCOP_01022;HBKHOP_02600;JHLLHD_02607;JPKDEA_02603;KBDKBJ_02555;LPHLDL_02465;NNICCC_00255;NPGDHH_01380;OAHHLH_06598;OMNKFL_02673;PJCLAL_02180 N-glycosyltransferase
37 group_5100 gene_presence_absence group_5100 group_5100 | SAOUHSC_02531 | none confidence group_5100 SF3 helicase domain-containing protein SAOUHSC_02531 hypothetical protein none 26.54 1.03 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=26.54; coverage=1.03 18 50 0.3600 0 50 0.0000 cases (MRSA) 3.63 57.4923 3.348-987.4 3.3475 987.412 1.48e-05 13.6750 Panaroo/Bakta+GenBank nucleotide_similarity 2333690..2334901 matched_representative_sequence=group_5100 BBHJIH_02596;CCGLPJ_01544;CNMMKL_01936;DGCAMH_01214;DHHPLE_02457;DPEBLA_01170;EBFKMK_01390;GNNCOP_01023;HBKHOP_02599;JHLLHD_02606;JPKDEA_02604;KBDKBJ_02556;LPHLDL_02464;NNICCC_00256;NPGDHH_01381;OAHHLH_06599;OMNKFL_02674;PJCLAL_02181 hypothetical protein
38 group_320 gene_presence_absence ccrC group_320 | SAOUHSC_01273 | none confidence ccrC Staphylococcal casette chromosome site specific recombinase CcrC SAOUHSC_01273 mutL DNA mismatch repair protein none 99.15 34.13 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=99.15; coverage=34.13 18 50 0.3600 0 50 0.0000 cases (MRSA) 3.63 57.4923 3.348-987.4 3.3475 987.412 1.48e-05 13.6750 Panaroo/Bakta+GenBank nucleotide_similarity 1229312..1231321 matched_representative_sequence=group_3205 BBHJIH_02594;CCGLPJ_01542;CNMMKL_01935;DGCAMH_01212;DHHPLE_02455;DPEBLA_01171;EBFKMK_01388;GNNCOP_01025;HBKHOP_02597;JHLLHD_02604;JPKDEA_02606;KBDKBJ_02557;LPHLDL_02462;NNICCC_00257;NPGDHH_01382;OAHHLH_06601;OMNKFL_02676;PJCLAL_02183 DNA mismatch repair protein
39 group_880 gene_presence_absence group_880 group_880 | SAOUHSC_00003 | none confidence group_880 hypothetical protein SAOUHSC_00003 hypothetical protein none 39.53 11.83 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=39.53; coverage=11.83 18 50 0.3600 0 50 0.0000 cases (MRSA) 3.63 57.4923 3.348-987.4 3.3475 987.412 1.58e-05 13.6466 Panaroo/Bakta+GenBank nucleotide_similarity 3670..3915 matched_representative_sequence=group_8805 BBHJIH_02618;CCGLPJ_01530;CNMMKL_01922;DGCAMH_02706;DHHPLE_02443;EBFKMK_01376;FJPBEI_02133;GNNCOP_02694;HBKHOP_02622;JHLLHD_02649;JPKDEA_02620;KBDKBJ_02754;LPHLDL_02450;NNICCC_00269;NPGDHH_02731;OAHHLH_06614;OMNKFL_02689;PJCLAL_02762 hypothetical protein
40 group_5703 gene_presence_absence ;tnp group_5703 | no_reference_locus | none confidence ;tnp hypothetical protein;IS6 family IS431mec transposase none Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. no sequence identity/coverage evidence available 17 50 0.3400 0 50 0.0000 cases (MRSA) 3.55 52.7612 3.068-907.5 3.06753 907.486 3.37e-05 13.1938 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. BBHJIH_02621;CCGLPJ_01533;CNMMKL_01925;DGCAMH_02709;DHHPLE_02446;EBFKMK_01379;FJPBEI_02136;HBKHOP_02625;JHLLHD_02652;JPKDEA_02623;LPHLDL_02453;MGNIJD_00601;NKBKLH_02725;NNICCC_00266;OAHHLH_06611;OMNKFL_02692;PJCLAL_02765 hypothetical protein;IS6 family IS431mec transposase
41 group_5119 gene_presence_absence group_5119 group_5119 | no_reference_locus | none confidence group_5119 Phage protein;hypothetical protein none No confident reference gene assignment; report the stable Panaroo cluster ID. no sequence identity/coverage evidence available 43 50 0.8600 13 50 0.2600 cases (MRSA) 2.41 16.1111 5.964-43.52 5.96413 43.5215 1.26e-06 12.9096 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. AAFANJ_02602;AGNJKP_02366;BBHJIH_02139;BGHJOB_02213;CKFMFB_01054;CNMMKL_00098;DBPPGI_02334;DGCAMH_02751;DHHPLE_02136;DPEBLA_01882;EAMBND_02595;EBFKMK_02739;EBHIAF_01862;EDBMEK_00445;EFOOKO_02377;FCNEHE_02077;FHJCBG_02295;FHPENM_01770;FIIBJA_02048;FJPBEI_02971;FMAEJP_02036;FMOEEE_00559;GEIAPO_02536;GGEFGC_02304;GGOGND_02263;GHNMBF_02185;GLHECH_01366;GNKNJO_02376;GNNCOP_01034;HBKHOP_02227 Phage protein;hypothetical protein
42 group_1274 gene_presence_absence group_1274 group_1274 | SAOUHSC_02194 | none confidence group_1274 hypothetical protein;DEAD/DEAH box helicase domain protein SAOUHSC_02194 HK97 family phage portal protein none 18.58 0.88 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=18.58; coverage=0.88 16 50 0.3200 0 50 0.0000 cases (MRSA) 3.44 48.3043 2.803-832.3 2.80349 832.287 6.55e-05 12.7778 Panaroo/Bakta+GenBank nucleotide_similarity complement(2053915..2055105) matched_representative_sequence=group_1274 BBHJIH_02390;CCGLPJ_01140;CNMMKL_01944;DGCAMH_01207;DHHPLE_02432;EBFKMK_01365;HBKHOP_02437;JHLLHD_02321;JPKDEA_02388;KBDKBJ_02549;LPHLDL_02439;NNICCC_00248;NPGDHH_01374;OAHHLH_06626;OMNKFL_02462;PJCLAL_01206 HK97 family phage portal protein
43 group_5422 gene_presence_absence group_5422 group_5422 | SAOUHSC_00378 | none confidence group_5422 Transposase;hypothetical protein SAOUHSC_00378 hypothetical protein none 82.16 14.54 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=82.16; coverage=14.54 32 50 0.6400 5 50 0.1000 cases (MRSA) 2.61 14.5332 5.071-41.65 5.07059 41.6546 1.61e-06 12.6545 Panaroo/Bakta+GenBank nucleotide_similarity complement(385390..385662) matched_representative_sequence=group_5422 BBHJIH_00004;BCINDJ_00004;BGHJOB_02841;DBPPGI_00361;DHHPLE_01200;DPEBLA_02232;EAMBND_02306;EBHIAF_02014;EDBMEK_00359;EEPHOB_00544;EFOOKO_02253;FCNEHE_02270;FHPENM_00374;FJPBEI_01778;FMOEEE_02300;GGEFGC_00361;GGOGND_00760;GHNMBF_00360;GNKNJO_02247;HBKHOP_01199;HGFBEP_02418;HJFIGM_00649;HJGKNO_00359;IHKMFK_01004;ILJMML_00391;JHLLHD_01084;JPKDEA_00657;KOFDAJ_02557;LPHLDL_01233;NBILEO_02582 hypothetical protein
44 group_2369 gene_presence_absence group_2369 group_2369 | SAOUHSC_00645 | none confidence group_2369 Phage protein;hypothetical protein SAOUHSC_00645 glycerol-3-phosphate cytidylyltransferase none 45.11 7.35 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=45.11; coverage=7.35 47 50 0.9400 19 50 0.3800 cases (MRSA) 2.69 21.9231 6.448-74.53 6.44846 74.5327 6.61e-06 12.6342 Panaroo/Bakta+GenBank nucleotide_similarity 634015..634413 matched_representative_sequence=12_refound_28 12_refound_28;14_refound_42_pseudo;27_refound_124;60_refound_391;62_refound_406_pseudo;63_refound_416;70_refound_454;74_refound_476_pseudo;75_refound_483;76_refound_492_pseudo;77_refound_504_pseudo;82_refound_524;84_refound_542;85_refound_546;86_refound_553;87_refound_557;94_refound_596;95_refound_603_pseudo;AAFANJ_02585;ADDHAP_02084;BCINDJ_02212;BGHJOB_02234;CCGLPJ_01814;CNMMKL_00117;DBPPGI_02561;DGCAMH_02340;DPEBLA_01896;EAMBND_02611;EBFKMK_02687;EBHIAF_01881 glycerol-3-phosphate cytidylyltransferase
45 group_1360 gene_presence_absence SAOUHSC_01932-like (group_1360) group_1360 | SAOUHSC_01932 | low confidence group_1360 Restriction endonuclease subunit S SAOUHSC_01932 type I restriction-modification system subunitS low 66.78 51.06 Low-confidence locus-level GenBank rescue. identity=66.78; coverage=51.06 20 50 0.4000 1 50 0.0200 cases (MRSA) 2.83 22.1803 3.979-123.6 3.97912 123.637 9.29e-06 12.5032 Panaroo/Bakta+GenBank nucleotide_similarity complement(1839335..1840534) matched_representative_sequence=60_refound_388 59_refound_383_pseudo;60_refound_388;82_refound_522;84_refound_538;89_refound_565_pseudo;90_refound_569_pseudo;94_refound_593;BGHJOB_02837;DPEBLA_02379;EDBMEK_00363;EFOOKO_02257;FHPENM_00378;FMOEEE_02296;GGOGND_00764;GHNMBF_00364;HFICCC_03178;HJGKNO_00363;ILJMML_00395;NJAOBP_04458;NKBKLH_02759;NMHDHA_00365 type I restriction-modification system subunitS
46 ptpB gene_presence_absence SAOUHSC_02356 (ptpB) ptpB | SAOUHSC_02356 | high confidence ptpB Low molecular weight protein-tyrosine-phosphatase PtpB SAOUHSC_02356 hypothetical protein high 99.64 99.05 High-confidence locus-level GenBank rescue. identity=99.64; coverage=99.05 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(2178210..2178629) matched_representative_sequence=ptpB AAFANJ_02220;ADDHAP_02387;AGNJKP_02258;BBHJIH_02337;BCINDJ_02438;BGHJOB_02499;BLNHMO_02421;CCGLPJ_02487;CDDCHJ_02368;CIALCM_02439;CJJPLC_02292;CKFMFB_01686;CNMMKL_02025;DBPPGI_02124;DGCAMH_02399;DHHPLE_02334;DNJFEH_01679;DPEBLA_02043;EAMBND_01697;EBFKMK_02217;EBHIAF_02413;EDBMEK_02157;EEPHOB_02119;EFOOKO_02102;EOFOFH_02418;FDFIHM_02495;FHJCBG_02190;FHPENM_02514;FIIBJA_02422;FJPBEI_01472 hypothetical protein
47 group_8769 gene_presence_absence group_8769 group_8769 | SAOUHSC_00012 | none confidence group_8769 hypothetical protein SAOUHSC_00012 hypothetical protein none 29.08 5.98 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=29.08; coverage=5.98 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 15414..15743 matched_representative_sequence=group_8769 AAFANJ_00311;ADDHAP_00693;AGNJKP_01682;BBHJIH_00354;BCINDJ_00446;BGHJOB_01007;BLNHMO_01113;CCGLPJ_00860;CDDCHJ_01838;CIALCM_00718;CJJPLC_01205;CKFMFB_00530;CNMMKL_01311;DBPPGI_00012;DGCAMH_00546;DHHPLE_00851;DNJFEH_00046;DPEBLA_00303;EAMBND_01898;EBFKMK_00438;EBHIAF_01349;EDBMEK_00012;EEPHOB_00894;EFOOKO_01188;EOFOFH_00283;FDFIHM_01176;FHJCBG_01665;FHPENM_00028;FIIBJA_00043;FJPBEI_01847 hypothetical protein
48 group_4339 gene_presence_absence group_4339 group_4339 | SAOUHSC_01918 | none confidence group_4339 Putative lipoprotein;Endonuclease SAOUHSC_01918 hypothetical protein none 85.94 8.46 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=85.94; coverage=8.46 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 1826667..1827317 matched_representative_sequence=group_4339 AAFANJ_02368;ADDHAP_02255;AGNJKP_01978;BBHJIH_00010;BCINDJ_00010;BGHJOB_02850;BLNHMO_02281;CCGLPJ_02339;CDDCHJ_02465;CIALCM_02299;CJJPLC_02179;CKFMFB_02034;CNMMKL_01657;DBPPGI_00353;DGCAMH_02115;DHHPLE_01194;DNJFEH_02349;DPEBLA_02224;EAMBND_02314;EBFKMK_00096;EBHIAF_02020;EDBMEK_00351;EEPHOB_00550;EFOOKO_02245;EOFOFH_02303;FDFIHM_02355;FHJCBG_02003;FHPENM_00366;FIIBJA_02509;FJPBEI_01772 hypothetical protein
49 group_4309 gene_presence_absence group_4309 group_4309 | SAOUHSC_01123 | none confidence group_4309 DNA-binding protein SAOUHSC_01123 hypothetical protein none 81.69 10.95 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=81.69; coverage=10.95 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 1078148..1078372 matched_representative_sequence=group_4309 AAFANJ_00605;ADDHAP_00179;AGNJKP_01059;BBHJIH_00642;BCINDJ_02571;BGHJOB_00608;BLNHMO_00037;CCGLPJ_00565;CDDCHJ_00086;CIALCM_01339;CJJPLC_00904;CKFMFB_01869;CNMMKL_02511;DBPPGI_01070;DGCAMH_00250;DHHPLE_00562;DNJFEH_02718;DPEBLA_01326;EAMBND_00432;EBFKMK_00733;EBHIAF_01088;EDBMEK_01071;EEPHOB_02506;EFOOKO_01696;EOFOFH_00577;FDFIHM_00101;FHJCBG_00443;FHPENM_01152;FIIBJA_00337;FJPBEI_02491 hypothetical protein
50 group_4304 gene_presence_absence sdpA; group_4304 | SAOUHSC_01900 | none confidence sdpA; CPBP family intramembrane metalloprotease SdpA;hypothetical protein SAOUHSC_01900 hypothetical protein none 73.27 2.67 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=73.27; coverage=2.67 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 1810087..1810722 matched_representative_sequence=group_4304 AAFANJ_02387;ADDHAP_02273;AGNJKP_01963;BBHJIH_00027;BCINDJ_00028;BGHJOB_02434;BLNHMO_02265;CCGLPJ_02321;CDDCHJ_01424;CIALCM_02283;CJJPLC_02195;CKFMFB_02019;CNMMKL_01642;DBPPGI_00337;DGCAMH_02097;DHHPLE_01177;DNJFEH_02365;DPEBLA_02209;EAMBND_02335;EBFKMK_00114;EBHIAF_02038;EDBMEK_00336;EEPHOB_00568;EFOOKO_00863;EOFOFH_02321;FDFIHM_02339;FHJCBG_01988;FHPENM_00351;FIIBJA_02490;FJPBEI_02672 hypothetical protein
51 group_4060 gene_presence_absence group_4060 group_4060 | SAOUHSC_00606 | none confidence group_4060 DUF4909 domain-containing protein SAOUHSC_00606 hypothetical protein none 19.79 3.11 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=19.79; coverage=3.11 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 597925..599220 matched_representative_sequence=group_4060 AAFANJ_02369;ADDHAP_02256;AGNJKP_01977;BBHJIH_00011;BCINDJ_00011;BGHJOB_02851;BLNHMO_02280;CCGLPJ_02338;CDDCHJ_02466;CIALCM_02298;CJJPLC_02180;CKFMFB_02033;CNMMKL_01656;DBPPGI_00352;DGCAMH_02114;DHHPLE_01193;DNJFEH_02350;DPEBLA_02223;EAMBND_02315;EBFKMK_00097;EBHIAF_02021;EDBMEK_00350;EEPHOB_00551;EFOOKO_02244;EOFOFH_02304;FDFIHM_02354;FHJCBG_02002;FHPENM_00365;FIIBJA_02508;FJPBEI_01771 hypothetical protein
52 group_3636 gene_presence_absence SAOUHSC_00808-like (group_3636) group_3636 | SAOUHSC_00808 | medium confidence group_3636 DUF5067 domain-containing protein;hypothetical protein SAOUHSC_00808 hypothetical protein medium 99.73 77.50 Medium-confidence locus-level GenBank rescue. identity=99.73; coverage=77.50 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(790206..790934) matched_representative_sequence=group_3636 AAFANJ_00954;ADDHAP_01495;AGNJKP_01267;BBHJIH_00929;BBHJIH_00930;BCINDJ_01160;BGHJOB_00302;BLNHMO_00326;CCGLPJ_00276;CDDCHJ_00955;CIALCM_01050;CJJPLC_00615;CKFMFB_01322;CNMMKL_00293;DBPPGI_01660;DGCAMH_01854;DHHPLE_00276;DHHPLE_00277;DNJFEH_01225;DPEBLA_01504;EAMBND_00121;EBFKMK_02120;EBHIAF_00212;EDBMEK_01158;EEPHOB_01527;EFOOKO_00200;EOFOFH_01748;FDFIHM_00390;FHJCBG_00153;FHPENM_01907 hypothetical protein
53 sel26 gene_presence_absence ;sel26 sel26 | SAOUHSC_01705 | none confidence ;sel26 hypothetical protein;staphylococcal enterotoxin type 26;Enterotoxin SAOUHSC_01705 enterotoxin family protein none 87.14 11.07 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=87.14; coverage=11.07 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(1611370..1612074) matched_representative_sequence=sel26 AAFANJ_00155;ADDHAP_00539;AGNJKP_01525;AGNJKP_01526;BBHJIH_00194;BBHJIH_00195;BCINDJ_00201;BCINDJ_00202;BGHJOB_00787;BLNHMO_01488;CCGLPJ_01012;CCGLPJ_01013;CDDCHJ_01255;CIALCM_01497;CJJPLC_01700;CKFMFB_01575;CNMMKL_01828;CNMMKL_01829;DBPPGI_00164;DBPPGI_00165;DGCAMH_00699;DGCAMH_00700;DHHPLE_01009;DHHPLE_01010;DNJFEH_00264;DPEBLA_00083;EAMBND_00272;EBFKMK_00283;EBFKMK_00284;EBHIAF_01504 enterotoxin family protein
54 emp gene_presence_absence ;emp emp | SAOUHSC_00816 | none confidence ;emp Extracellular matrix protein-binding protein emp;extracellular matrix protein-binding adhesin Emp SAOUHSC_00816 extracellular matrix and plasma binding protein none 90.68 7.12 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=90.68; coverage=7.12 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 797866..798888 matched_representative_sequence=emp AAFANJ_00949;ADDHAP_01489;AGNJKP_01262;BBHJIH_00924;BCINDJ_01165;BGHJOB_00307;BLNHMO_00321;CCGLPJ_00281;CDDCHJ_00961;CIALCM_01055;CJJPLC_00620;CKFMFB_01327;CNMMKL_00299;DBPPGI_00792;DGCAMH_01849;DHHPLE_00282;DNJFEH_01220;DPEBLA_02699;EAMBND_00116;EBFKMK_02125;EBHIAF_00206;EDBMEK_01824;EEPHOB_01522;EFOOKO_00195;EOFOFH_01743;FDFIHM_00385;FHJCBG_00158;FHPENM_01691;FIIBJA_00682;FJPBEI_00234 extracellular matrix and plasma binding protein
55 group_2809 gene_presence_absence group_2809 group_2809 | SAOUHSC_00684 | none confidence group_2809 N-acetyltransferase domain-containing protein SAOUHSC_00684 hypothetical protein none 96.64 16.67 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=96.64; coverage=16.67 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 670865..671308 matched_representative_sequence=group_2809 AAFANJ_01084;ADDHAP_01611;AGNJKP_01380;BBHJIH_01044;BCINDJ_01045;BGHJOB_00188;BLNHMO_00441;CCGLPJ_00163;CDDCHJ_00842;CIALCM_00935;CJJPLC_00500;CKFMFB_01208;CNMMKL_00178;DBPPGI_01547;DGCAMH_01967;DHHPLE_00162;DNJFEH_02270;DPEBLA_01615;EAMBND_00257;EBFKMK_02007;EBHIAF_00328;EDBMEK_01271;EEPHOB_01581;EFOOKO_00313;EOFOFH_01860;FDFIHM_00505;FHJCBG_00038;FHPENM_02020;FIIBJA_00817;FJPBEI_00354 hypothetical protein
56 group_2799 gene_presence_absence SAOUHSC_00810-like (group_2799) group_2799 | SAOUHSC_00810 | low confidence group_2799 hypothetical protein;SMODS-associated and fused to various effectors domain-containing protein SAOUHSC_00810 hypothetical protein low 99.23 50.96 Low-confidence locus-level GenBank rescue. identity=99.23; coverage=50.96 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 791533..792054 matched_representative_sequence=group_2799 AAFANJ_00953;ADDHAP_01494;AGNJKP_01266;BBHJIH_00928;BCINDJ_01161;BGHJOB_00303;BLNHMO_00325;CCGLPJ_00277;CDDCHJ_00956;CDDCHJ_00957;CIALCM_01051;CJJPLC_00616;CKFMFB_01323;CNMMKL_00294;CNMMKL_00295;DBPPGI_01661;DGCAMH_01853;DHHPLE_00278;DNJFEH_01224;DPEBLA_02695;EAMBND_00120;EBFKMK_02121;EBHIAF_00211;EDBMEK_01157;EEPHOB_01526;EFOOKO_00199;EOFOFH_01747;FDFIHM_00389;FHJCBG_00154;FHPENM_01906 hypothetical protein
57 group_2757 gene_presence_absence group_2757 group_2757 | SAOUHSC_02957 | none confidence group_2757 hypothetical protein SAOUHSC_02957 hypothetical protein none 95.52 29.35 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=95.52; coverage=29.35 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(2719286..2719486) matched_representative_sequence=group_2757 AAFANJ_01791;ADDHAP_01842;AGNJKP_00218;BBHJIH_01313;BCINDJ_01981;BGHJOB_02018;BLNHMO_00744;CCGLPJ_01672;CDDCHJ_01102;CIALCM_00323;CJJPLC_00131;CKFMFB_02139;CNMMKL_01177;DBPPGI_01274;DGCAMH_01343;DHHPLE_01311;DNJFEH_02207;DPEBLA_01051;EAMBND_00755;EBFKMK_01519;EBHIAF_00621;EDBMEK_01498;EEPHOB_00407;EFOOKO_01327;EOFOFH_01324;FDFIHM_00807;FHJCBG_01221;FHPENM_01369;FIIBJA_01510;FJPBEI_01930 hypothetical protein
58 group_2639 gene_presence_absence SAOUHSC_01134-like (group_2639) group_2639 | SAOUHSC_01134 | low confidence group_2639 DNA-binding protein SAOUHSC_01134 hypothetical protein low 95.09 46.97 Low-confidence locus-level GenBank rescue. identity=95.09; coverage=46.97 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 1087343..1087531 matched_representative_sequence=group_2639 AAFANJ_00594;ADDHAP_00169;AGNJKP_01048;BBHJIH_00632;BCINDJ_02561;BGHJOB_00618;BLNHMO_00027;CCGLPJ_00575;CDDCHJ_00095;CIALCM_01349;CJJPLC_00914;CKFMFB_01879;CNMMKL_02501;DBPPGI_01079;DGCAMH_00260;DHHPLE_00572;DNJFEH_02728;DPEBLA_01316;EAMBND_00442;EBFKMK_00723;EBHIAF_01098;EDBMEK_01062;EEPHOB_02496;EFOOKO_01687;EOFOFH_00567;FDFIHM_00091;FHJCBG_00453;FHPENM_01143;FIIBJA_00326;FJPBEI_02501 hypothetical protein
59 group_2551 gene_presence_absence group_2551 group_2551 | SAOUHSC_02892 | none confidence group_2551 hypothetical protein SAOUHSC_02892 hypothetical protein none 72.51 13.08 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=72.51; coverage=13.08 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 2664225..2664725 matched_representative_sequence=group_2551 AAFANJ_01844;ADDHAP_01895;AGNJKP_00165;BBHJIH_01367;BCINDJ_01532;BGHJOB_01967;BLNHMO_00691;CCGLPJ_01724;CDDCHJ_01051;CIALCM_00376;CJJPLC_00078;CKFMFB_02085;CNMMKL_02458;DBPPGI_01327;DGCAMH_01395;DHHPLE_01365;DNJFEH_01834;DPEBLA_02688;EAMBND_02384;EBFKMK_01571;EBHIAF_00567;EDBMEK_01445;EEPHOB_00461;EFOOKO_01275;EOFOFH_01375;FDFIHM_00754;FHJCBG_01275;FHPENM_01421;FIIBJA_01457;FJPBEI_02179 hypothetical protein
60 group_2387 gene_presence_absence tagX group_2387 | SAOUHSC_00644 | none confidence tagX Putative glycosyltransferase TagX SAOUHSC_00644 glycosyltransferase TagX none 97.74 14.88 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=97.74; coverage=14.88 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 632891..633952 matched_representative_sequence=group_2387 AAFANJ_01120;ADDHAP_01647;AGNJKP_01416;BBHJIH_01080;BCINDJ_01009;BGHJOB_00151;BLNHMO_00477;CCGLPJ_00127;CDDCHJ_00791;CIALCM_00899;CJJPLC_00464;CKFMFB_02422;CNMMKL_00079;DBPPGI_01511;DGCAMH_02003;DHHPLE_00126;DNJFEH_02306;DPEBLA_02523;EAMBND_00912;EBFKMK_01971;EBHIAF_00364;EDBMEK_01307;EEPHOB_01545;EFOOKO_00349;EOFOFH_01896;FDFIHM_00541;FHJCBG_00002;FHPENM_02056;FIIBJA_00853;FJPBEI_00390 glycosyltransferase TagX
61 group_2132 gene_presence_absence group_2132 group_2132 | SAOUHSC_02726 | none confidence group_2132 Bacterial transcription activator effector binding domain-containing protein;hypothetical protein SAOUHSC_02726 hypothetical protein none 96.41 21.31 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=96.41; coverage=21.31 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(2506882..2507355) matched_representative_sequence=group_2132 AAFANJ_01986;ADDHAP_01395;AGNJKP_00026;BBHJIH_01507;BCINDJ_01673;BGHJOB_01891;BLNHMO_02161;CCGLPJ_02010;CDDCHJ_00636;CIALCM_02187;CJJPLC_01511;CKFMFB_00216;CNMMKL_00561;DBPPGI_01726;DGCAMH_01540;DHHPLE_01505;DNJFEH_01317;DPEBLA_01679;EAMBND_01082;EBFKMK_01649;EBHIAF_01756;EDBMEK_01889;EEPHOB_01280;EFOOKO_01994;EOFOFH_01658;FDFIHM_01700;FHJCBG_01417;FHPENM_02396;FIIBJA_01735;FJPBEI_01226 hypothetical protein
62 group_1942 gene_presence_absence group_1942 group_1942 | SAOUHSC_02925 | none confidence group_1942 hypothetical protein SAOUHSC_02925 hypothetical protein none 96.88 21.58 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=96.88; coverage=21.58 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 2691116..2691532 matched_representative_sequence=group_1942 AAFANJ_01812;ADDHAP_01862;AGNJKP_00197;BBHJIH_01334;BCINDJ_01960;BGHJOB_01997;BLNHMO_00723;CCGLPJ_01694;CDDCHJ_01081;CIALCM_00344;CJJPLC_00110;CKFMFB_02118;CNMMKL_01198;DBPPGI_01296;DGCAMH_01365;DHHPLE_01332;DNJFEH_02228;DPEBLA_01029;EAMBND_00733;EBFKMK_01541;EBHIAF_00600;EDBMEK_01476;EEPHOB_00428;EFOOKO_01305;EOFOFH_01345;FDFIHM_00786;FHJCBG_01243;FHPENM_01391;FIIBJA_01489;FJPBEI_02636 hypothetical protein
63 group_1933 gene_presence_absence group_1933 group_1933 | SAOUHSC_01595 | none confidence group_1933 Phage protein SAOUHSC_01595 hypothetical protein none 87.55 12.45 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=87.55; coverage=12.45 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(1520234..1520482) matched_representative_sequence=group_1933 AAFANJ_00255;ADDHAP_00638;AGNJKP_01625;BBHJIH_00298;BCINDJ_00302;BGHJOB_00885;BLNHMO_01389;CCGLPJ_00914;CDDCHJ_01956;CIALCM_01398;CJJPLC_01799;CKFMFB_02477;CNMMKL_01431;DBPPGI_00067;DGCAMH_00600;DHHPLE_00906;DNJFEH_00165;DPEBLA_00181;EAMBND_01762;EBFKMK_00383;EBHIAF_01404;EDBMEK_00067;EEPHOB_00838;EFOOKO_01132;EOFOFH_00227;FDFIHM_01783;FHJCBG_01720;FHPENM_00083;FIIBJA_02117;FJPBEI_02277 hypothetical protein
64 group_1854 gene_presence_absence group_1854 group_1854 | SAOUHSC_02104 | none confidence group_1854 Cytosolic protein SAOUHSC_02104 hypothetical protein none 96.14 19.32 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=96.14; coverage=19.32 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(1978643..1979056) matched_representative_sequence=group_1854 AAFANJ_02433;ADDHAP_02004;AGNJKP_02498;BBHJIH_02252;BCINDJ_02128;BGHJOB_02316;BLNHMO_02000;CCGLPJ_01915;CDDCHJ_02031;CIALCM_02086;CJJPLC_02363;CKFMFB_01169;CNMMKL_01889;DBPPGI_02207;DGCAMH_02240;DHHPLE_02249;DNJFEH_01590;DPEBLA_01979;EAMBND_02112;EBFKMK_02389;EBHIAF_01963;EDBMEK_02243;EEPHOB_01879;EFOOKO_02203;EOFOFH_02053;FDFIHM_02186;FHJCBG_02384;FHPENM_01873;FIIBJA_01948;FJPBEI_02304 hypothetical protein
65 group_1747 gene_presence_absence SAOUHSC_00704-like (group_1747) group_1747 | SAOUHSC_00704 | medium confidence group_1747 Lipoprotein SAOUHSC_00704 hypothetical protein medium 98.47 77.20 Medium-confidence locus-level GenBank rescue. identity=98.47; coverage=77.20 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 688884..689336 matched_representative_sequence=group_1747 AAFANJ_01064;ADDHAP_01591;AGNJKP_01360;BBHJIH_01024;BCINDJ_01065;BGHJOB_00208;BLNHMO_00421;CCGLPJ_00183;CDDCHJ_00862;CIALCM_00955;CJJPLC_00520;CKFMFB_01228;CNMMKL_00198;DBPPGI_01567;DGCAMH_01947;DHHPLE_00182;DNJFEH_02581;DPEBLA_01595;EAMBND_00237;EBFKMK_02027;EBHIAF_00308;EDBMEK_01251;EEPHOB_01602;EFOOKO_00293;EOFOFH_01840;FDFIHM_00485;FHJCBG_00058;FHPENM_02000;FIIBJA_00797;FJPBEI_00334 hypothetical protein
66 group_1673 gene_presence_absence group_1673 group_1673 | SAOUHSC_01764 | none confidence group_1673 Type III leader peptidase family protein SAOUHSC_01764 hypothetical protein none 98.31 22.32 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=98.31; coverage=22.32 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(1663415..1664122) matched_representative_sequence=group_1673 AAFANJ_00102;ADDHAP_00487;AGNJKP_01474;BBHJIH_00141;BCINDJ_00142;BGHJOB_00736;BLNHMO_01541;CCGLPJ_01065;CDDCHJ_01307;CIALCM_01550;CJJPLC_01647;CKFMFB_01629;CNMMKL_00724;DBPPGI_00218;DGCAMH_00752;DHHPLE_01063;DNJFEH_00317;DPEBLA_00029;EAMBND_00325;EBFKMK_00231;EBHIAF_01560;EDBMEK_00217;EEPHOB_00683;EFOOKO_00982;EOFOFH_00075;FDFIHM_01935;FHJCBG_01869;FHPENM_00233;FIIBJA_02270;FJPBEI_00531 hypothetical protein
67 group_1613 gene_presence_absence group_1613 group_1613 | SAOUHSC_02650 | none confidence group_1613 Serine protease HtrA-like SAOUHSC_02650 hypothetical protein none 24.69 0.65 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=24.69; coverage=0.65 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(2436751..2437380) matched_representative_sequence=group_1613 AAFANJ_00746;ADDHAP_00322;AGNJKP_02536;BBHJIH_00785;BCINDJ_01376;BGHJOB_00465;BLNHMO_00178;CCGLPJ_00424;CDDCHJ_02163;CIALCM_01198;CJJPLC_00763;CKFMFB_00853;CNMMKL_00435;DBPPGI_00930;DGCAMH_00110;DHHPLE_00421;DNJFEH_00818;DPEBLA_00869;EAMBND_02177;EBFKMK_00873;EBHIAF_02248;EDBMEK_01686;EEPHOB_01383;EFOOKO_00056;EOFOFH_00717;FDFIHM_00242;FHJCBG_00301;FHPENM_01553;FIIBJA_00477;FJPBEI_01092 hypothetical protein
68 group_1571 gene_presence_absence group_1571 group_1571 | SAOUHSC_00237 | none confidence group_1571 SAM-dependent methyltransferase SAOUHSC_00237 hypothetical protein none 95.54 10.24 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=95.54; coverage=10.24 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(258896..259657) matched_representative_sequence=group_1571 AAFANJ_01451;ADDHAP_00892;AGNJKP_00552;BBHJIH_01923;BCINDJ_00792;BGHJOB_01490;BLNHMO_01061;CCGLPJ_01327;CDDCHJ_01468;CIALCM_00006;CJJPLC_00449;CKFMFB_00645;CNMMKL_01032;DBPPGI_00601;DGCAMH_01020;DHHPLE_01938;DNJFEH_00326;DPEBLA_00618;EAMBND_00616;EBFKMK_01178;EBHIAF_00948;EDBMEK_00637;EEPHOB_00107;EFOOKO_00663;EOFOFH_01018;FDFIHM_01124;FHJCBG_00921;FHPENM_00726;FIIBJA_01167;FJPBEI_01887 hypothetical protein
69 scdA gene_presence_absence scdA scdA | SAOUHSC_00229 | none confidence scdA Iron-sulfur cluster repair protein ScdA SAOUHSC_00229 cell wall biosynthesis protein ScdA none 98.81 26.67 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=98.81; coverage=26.67 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 250591..251265 matched_representative_sequence=scdA AAFANJ_01460;ADDHAP_00900;AGNJKP_00542;BBHJIH_01914;BCINDJ_00801;BGHJOB_01481;BLNHMO_01052;CCGLPJ_01318;CDDCHJ_01459;CIALCM_00015;CJJPLC_00440;CKFMFB_00635;CNMMKL_01022;DBPPGI_00609;DGCAMH_01029;DHHPLE_01947;DNJFEH_00335;DPEBLA_00626;EAMBND_00625;EBFKMK_01187;EBHIAF_00939;EDBMEK_00629;EEPHOB_00115;EFOOKO_00655;EOFOFH_01027;FDFIHM_01115;FHJCBG_00931;FHPENM_00734;FIIBJA_01158;FJPBEI_01896 cell wall biosynthesis protein ScdA
70 group_1455 gene_presence_absence group_1455 group_1455 | SAOUHSC_02973 | none confidence group_1455 Low-complexity protein;hypothetical protein SAOUHSC_02973 hypothetical protein none 65.17 6.12 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=65.17; coverage=6.12 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 2735412..2735870 matched_representative_sequence=group_1455 AAFANJ_01776;ADDHAP_01827;AGNJKP_00233;BBHJIH_01298;BCINDJ_01996;BGHJOB_02033;BLNHMO_00759;CCGLPJ_01657;CDDCHJ_01118;CIALCM_00308;CJJPLC_00146;CKFMFB_02154;CNMMKL_01162;DBPPGI_01258;DGCAMH_01328;DHHPLE_01296;DNJFEH_00998;DPEBLA_01066;EAMBND_00770;EBFKMK_01504;EBHIAF_00637;EDBMEK_01513;EEPHOB_00392;EFOOKO_01342;EOFOFH_01309;FDFIHM_00822;FHJCBG_01206;FHPENM_01354;FIIBJA_01525;FJPBEI_01946 hypothetical protein
71 group_1350 gene_presence_absence group_1350 group_1350 | SAOUHSC_01638 | none confidence group_1350 Competence protein ComGE SAOUHSC_01638 hypothetical protein none 94.69 30.00 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=94.69; coverage=30.00 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(1557239..1557559) matched_representative_sequence=group_1350 AAFANJ_00215;ADDHAP_00600;AGNJKP_01585;BBHJIH_00255;BCINDJ_00262;BGHJOB_00847;BLNHMO_01428;CCGLPJ_00952;CDDCHJ_01995;CIALCM_01437;CJJPLC_01760;CKFMFB_01515;CNMMKL_01766;DBPPGI_00105;DGCAMH_00638;DHHPLE_00949;DNJFEH_00204;DPEBLA_00143;EAMBND_01800;EBFKMK_00345;EBHIAF_01444;EDBMEK_00105;EEPHOB_00798;EFOOKO_01094;EOFOFH_00189;FDFIHM_01822;FHJCBG_01758;FHPENM_00121;FIIBJA_02157;FJPBEI_00409 hypothetical protein
72 group_1246 gene_presence_absence SAOUHSC_02129-like (group_1246) group_1246 | SAOUHSC_02129 | low confidence group_1246 Staphostatin A domain-containing protein SAOUHSC_02129 hypothetical protein low 98.17 42.51 Low-confidence locus-level GenBank rescue. identity=98.17; coverage=42.51 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 2003536..2003862 matched_representative_sequence=group_1246 AAFANJ_02454;ADDHAP_02025;AGNJKP_02477;BBHJIH_02231;BCINDJ_02149;BGHJOB_02295;BLNHMO_02021;CCGLPJ_01875;CDDCHJ_02052;CIALCM_02065;CJJPLC_02384;CKFMFB_01145;CNMMKL_01868;DBPPGI_02228;DGCAMH_02280;DHHPLE_02228;DNJFEH_01611;DPEBLA_01958;EAMBND_02134;EBFKMK_02429;EBHIAF_01942;EDBMEK_02264;EEPHOB_01900;EFOOKO_02182;EOFOFH_02074;FDFIHM_02207;FHJCBG_02405;FHPENM_01852;FIIBJA_01969;FJPBEI_01688 hypothetical protein
73 group_1203 gene_presence_absence ;vraA group_1203 | SAOUHSC_00144 | none confidence ;vraA hypothetical protein;Putative long chain fatty acid-CoA ligase VraA SAOUHSC_00144 hypothetical protein none 98.09 4.39 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=98.09; coverage=4.39 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 149045..156220 matched_representative_sequence=group_1203 AAFANJ_01534;ADDHAP_00974;AGNJKP_00460;BBHJIH_01833;BCINDJ_00882;BGHJOB_01407;BLNHMO_00966;CCGLPJ_01243;CDDCHJ_01782;CIALCM_00101;CJJPLC_00354;CKFMFB_00560;CNMMKL_01291;DBPPGI_00684;DGCAMH_01104;DHHPLE_02028;DNJFEH_00422;DPEBLA_00708;EAMBND_00700;EBFKMK_01262;EBHIAF_00856;EDBMEK_00554;EEPHOB_00196;EFOOKO_00580;EOFOFH_01102;FDFIHM_01029;FHJCBG_01005;FHPENM_00809;FIIBJA_01084;FJPBEI_00856 hypothetical protein
74 group_894 gene_presence_absence panB group_894 | SAOUHSC_02919 | none confidence panB 3-methyl-2-oxobutanoatehydroxymethyltransferase SAOUHSC_02919 panB 3-methyl-2-oxobutanoatehydroxymethyltransferase none 39.73 2.26 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=39.73; coverage=2.26 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(2683527..2684318) matched_representative_sequence=group_8942 AAFANJ_02109;ADDHAP_01275;AGNJKP_01833;BBHJIH_01628;BCINDJ_01793;BGHJOB_01767;BLNHMO_01759;CCGLPJ_02131;CDDCHJ_00516;CIALCM_01691;CJJPLC_01393;CKFMFB_00096;CNMMKL_01539;DBPPGI_01935;DGCAMH_01661;DHHPLE_01626;DNJFEH_00559;DPEBLA_01439;EAMBND_01361;EBFKMK_01770;EBHIAF_01636;EDBMEK_02087;EEPHOB_01158;EFOOKO_01798;EOFOFH_01537;FDFIHM_01582;FHJCBG_01539;FHPENM_02084;FIIBJA_01858;FJPBEI_00627 3-methyl-2-oxobutanoatehydroxymethyltransferase
75 scpA gene_presence_absence scpA scpA | SAOUHSC_02127 | none confidence scpA cysteine protease staphopain A SAOUHSC_02127 staphopain thiol proteinase none 98.29 13.02 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=98.29; coverage=13.02 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity 2002339..2003505 matched_representative_sequence=scpA AAFANJ_02453;ADDHAP_02024;AGNJKP_02478;BBHJIH_02232;BCINDJ_02148;BGHJOB_02296;BLNHMO_02020;CCGLPJ_01876;CDDCHJ_02051;CIALCM_02066;CJJPLC_02383;CKFMFB_01146;CNMMKL_01869;DBPPGI_02227;DGCAMH_02279;DHHPLE_02229;DNJFEH_01610;DPEBLA_01959;EAMBND_02133;EBFKMK_02428;EBHIAF_01943;EDBMEK_02263;EEPHOB_01899;EFOOKO_02183;EOFOFH_02073;FDFIHM_02206;FHJCBG_02404;FHPENM_01853;FIIBJA_01968;FJPBEI_01687 staphopain thiol proteinase
76 group_763 gene_presence_absence SAOUHSC_01622 (group_763) group_763 | SAOUHSC_01622 | high confidence group_763 hypothetical protein SAOUHSC_01622 hypothetical protein high 100.00 100.00 High-confidence locus-level GenBank rescue. identity=100.00; coverage=100.00 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_exact_or_contained complement(1544951..1545313) matched_representative_sequence=group_7635 AAFANJ_00024;ADDHAP_02315;AGNJKP_01927;BBHJIH_00064;BCINDJ_00065;BGHJOB_02393;BLNHMO_02224;CCGLPJ_02281;CDDCHJ_01386;CIALCM_02242;CJJPLC_02236;CKFMFB_02633;CNMMKL_00804;DBPPGI_00299;DGCAMH_02057;DHHPLE_01140;DNJFEH_02529;DPEBLA_02172;EAMBND_00404;EBFKMK_00154;EBHIAF_02097;EDBMEK_00298;EEPHOB_00605;EFOOKO_00901;EOFOFH_02361;FDFIHM_02298;FHJCBG_01949;FHPENM_00313;FIIBJA_02348;FJPBEI_02081 hypothetical protein
77 group_750 gene_presence_absence rpsI group_750 | SAOUHSC_02477 | none confidence rpsI 30S ribosomal protein S9 SAOUHSC_02477 rpsI 30S ribosomal protein S9 none 89.14 7.38 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=89.14; coverage=7.38 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_similarity complement(2299327..2299725) matched_representative_sequence=group_7500 AAFANJ_00149;ADDHAP_00535;AGNJKP_01521;BBHJIH_00188;BCINDJ_00195;BGHJOB_00782;BLNHMO_01494;CCGLPJ_01018;CDDCHJ_01259;CIALCM_01503;CJJPLC_01694;CKFMFB_01582;CNMMKL_01834;DBPPGI_00170;DGCAMH_00705;DHHPLE_01016;DNJFEH_00270;DPEBLA_00076;EAMBND_00278;EBFKMK_00278;EBHIAF_01512;EDBMEK_00170;EEPHOB_00731;EFOOKO_01029;EOFOFH_00122;FDFIHM_01888;FHJCBG_01822;FHPENM_00186;FIIBJA_02223;FJPBEI_00477 30S ribosomal protein S9
78 group_704 gene_presence_absence SAOUHSC_00659 (group_704) group_704 | SAOUHSC_00659 | high confidence group_704 YueH-like family protein SAOUHSC_00659 hypothetical protein high 100.00 100.00 High-confidence locus-level GenBank rescue. identity=100.00; coverage=100.00 50 50 1.0000 32 50 0.6400 cases (MRSA) 37.2 57.4923 3.348-987.4 3.3475 987.412 0.000304 12.3624 Panaroo/Bakta+GenBank nucleotide_exact_or_contained 646350..646847 matched_representative_sequence=group_7048 AAFANJ_00749;ADDHAP_00325;AGNJKP_02533;BBHJIH_00788;BCINDJ_01373;BGHJOB_00462;BLNHMO_00181;CCGLPJ_00421;CDDCHJ_02160;CIALCM_01195;CJJPLC_00760;CKFMFB_00856;CNMMKL_00432;DBPPGI_00927;DGCAMH_00107;DHHPLE_00418;DNJFEH_00821;DPEBLA_00866;EAMBND_02174;EBFKMK_00876;EBHIAF_02251;EDBMEK_01689;EEPHOB_01386;EFOOKO_00059;EOFOFH_00720;FDFIHM_00245;FHJCBG_00298;FHPENM_01556;FIIBJA_00480;FJPBEI_01095 hypothetical protein
79 group_5389 gene_presence_absence group_5389 group_5389 | SAOUHSC_00094 | none confidence group_5389 Phage protein;hypothetical protein SAOUHSC_00094 hypothetical protein none 22.03 1.01 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=22.03; coverage=1.01 15 50 0.3000 0 50 0.0000 cases (MRSA) 3.35 44.0986 2.554-761.4 2.55406 761.408 0.00014 12.3165 Panaroo/Bakta+GenBank nucleotide_similarity 100455..101054 matched_representative_sequence=group_5389 BBHJIH_02599;CCGLPJ_01547;DGCAMH_01217;DGCAMH_01218;DHHPLE_02460;EBFKMK_01393;EBFKMK_01394;GNNCOP_01020;HBKHOP_02602;JHLLHD_02609;JPKDEA_02601;KBDKBJ_02553;LPHLDL_02467;NPGDHH_01378;OAHHLH_06596;OMNKFL_02671;PJCLAL_02178 hypothetical protein
80 group_3396 gene_presence_absence ;rinB group_3396 | SAOUHSC_02053 | low confidence ;rinB hypothetical protein;RinB SAOUHSC_02053 transcriptional activator rinb-like protein low 79.06 44.00 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=79.06; coverage=44.00 39 50 0.7800 10 50 0.2000 cases (MRSA) 2.26 13.2484 5.152-34.07 5.15212 34.0678 2.67e-06 12.3012 Panaroo/Bakta+GenBank nucleotide_similarity complement(1951266..1951454) matched_representative_sequence=group_3396 AGNJKP_02347;BBHJIH_02159;BCINDJ_02213;BGHJOB_02233;CCGLPJ_01813;CNMMKL_00116;DBPPGI_02562;DGCAMH_02341;DHHPLE_02156;DPEBLA_01893;EBFKMK_02688;EDBMEK_02504;EFOOKO_02529;EOFOFH_02135;FHPENM_01789;FJPBEI_01751;FMAEJP_02020;GEIAPO_02552;GGEFGC_02533;GGOGND_02241;GHNMBF_02165;GNFCHG_02499;GNKNJO_02350;GNNCOP_01417;HBKHOP_02207;HFICCC_03524;HJFIGM_02017;HJGKNO_02392;IGAMFP_02138;ILJMML_02525 transcriptional activator rinb-like protein
81 group_8659 gene_presence_absence SAOUHSC_02190 (group_8659) group_8659 | SAOUHSC_02190 | high confidence group_8659 Bacteriophage SAOUHSC_02190 hypothetical protein high 100.00 100.00 High-confidence locus-level GenBank rescue. identity=100.00; coverage=100.00 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_exact_or_contained complement(2051809..2051967) matched_representative_sequence=group_8659 AGNJKP_02334;BBHJIH_02172;CKFMFB_01087;DBPPGI_02551;DHHPLE_02169;DPEBLA_01906;EAMBND_02521;EDBMEK_02493;EFOOKO_02540;FHJCBG_02266;FHPENM_01800;FMOEEE_02662;GGEFGC_02544;GHNMBF_02154;GNKNJO_02593;HBKHOP_02194;HFICCC_03513;HGAGGM_02639;HJGKNO_02381;ILJMML_02536;JHLLHD_02046;JPKDEA_02077;KOFDAJ_02494;LPHLDL_02198;MGNIJD_02516;NBILEO_02519;NCJOOM_02763;NJAOBP_03642;NPGDHH_02382;OAHHLH_04861 hypothetical protein
82 group_7790 gene_presence_absence SAOUHSC_02189-like (group_7790) group_7790 | SAOUHSC_02189 | medium confidence group_7790 DNA packaging protein SAOUHSC_02189 hypothetical protein medium 99.40 60.96 Medium-confidence locus-level GenBank rescue. identity=99.40; coverage=60.96 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(2051468..2051800) matched_representative_sequence=group_7790 AGNJKP_02333;BBHJIH_02173;CKFMFB_01088;DBPPGI_02550;DHHPLE_02170;DPEBLA_01907;EAMBND_02520;EDBMEK_02492;EFOOKO_02541;FHJCBG_02265;FHPENM_01801;FMOEEE_02663;GGEFGC_02545;GHNMBF_02153;GNKNJO_02594;HBKHOP_02193;HFICCC_03512;HGAGGM_02640;HJGKNO_02380;ILJMML_02537;JHLLHD_02045;JPKDEA_02076;KOFDAJ_02493;LPHLDL_02197;MGNIJD_02515;NBILEO_02518;NCJOOM_02762;NJAOBP_03643;NPGDHH_02381;OAHHLH_04860 hypothetical protein
83 group_7782 gene_presence_absence SAOUHSC_02188 (group_7782) group_7782 | SAOUHSC_02188 | high confidence group_7782 Head-tail adaptor SAOUHSC_02188 phage head-tail adaptor high 100.00 100.00 High-confidence locus-level GenBank rescue. identity=100.00; coverage=100.00 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_exact_or_contained complement(2051146..2051481) matched_representative_sequence=group_7782 AGNJKP_02332;BBHJIH_02174;CKFMFB_01089;DBPPGI_02549;DHHPLE_02171;DPEBLA_01908;EAMBND_02519;EDBMEK_02491;EFOOKO_02542;FHJCBG_02264;FHPENM_01802;FMOEEE_02664;GGEFGC_02546;GHNMBF_02152;GNKNJO_02595;HBKHOP_02192;HFICCC_03511;HGAGGM_02641;HJGKNO_02379;ILJMML_02538;JHLLHD_02044;JPKDEA_02075;KOFDAJ_02492;LPHLDL_02196;MGNIJD_02514;NBILEO_02517;NCJOOM_02761;NJAOBP_03644;NPGDHH_02380;OAHHLH_04859 phage head-tail adaptor
84 group_6751 gene_presence_absence SAOUHSC_02193 (group_6751) group_6751 | SAOUHSC_02193 | high confidence group_6751 Prohead protease SAOUHSC_02193 prohead protease high 100.00 100.00 High-confidence locus-level GenBank rescue. identity=100.00; coverage=100.00 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_exact_or_contained complement(2053338..2053922) matched_representative_sequence=group_6751 63_refound_409_pseudo;AGNJKP_02336;BBHJIH_02170;CKFMFB_01085;DBPPGI_02553;DHHPLE_02167;DPEBLA_01904;EAMBND_02523;EDBMEK_02495;EFOOKO_02538;FHJCBG_02268;FHPENM_01798;FMOEEE_02660;GGEFGC_02542;GHNMBF_02156;GNKNJO_02591;HBKHOP_02196;HFICCC_03515;HGAGGM_02637;HJGKNO_02383;ILJMML_02534;JHLLHD_02048;JPKDEA_02079;KOFDAJ_02496;LPHLDL_02200;MGNIJD_02518;NBILEO_02521;NJAOBP_03640;NPGDHH_02384;OAHHLH_04863 prohead protease
85 group_3641 gene_presence_absence group_3641 group_3641 | SAOUHSC_02185 | none confidence group_3641 BIG2 domain-containing protein;hypothetical protein SAOUHSC_02185 phi PVL orf 13-like protein none 87.53 5.56 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=87.53; coverage=5.56 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(2049438..2050391) matched_representative_sequence=group_3641 AGNJKP_02329;BBHJIH_02177;CKFMFB_01092;DBPPGI_02546;DHHPLE_02174;DPEBLA_01911;EAMBND_02516;EDBMEK_02488;EFOOKO_02545;FHJCBG_02261;FHPENM_01805;FMOEEE_02667;GGEFGC_02549;GHNMBF_02149;GNKNJO_02598;HBKHOP_02189;HFICCC_03508;HGAGGM_02644;HJGKNO_02376;ILJMML_02541;JHLLHD_02041;JPKDEA_02072;KOFDAJ_02489;LPHLDL_02193;MGNIJD_02511;NBILEO_02514;NCJOOM_02792;NJAOBP_03647;NPGDHH_02377;OAHHLH_04856 phi PVL orf 13-like protein
86 group_3377 gene_presence_absence group_3377 group_3377 | SAOUHSC_02184 | none confidence group_3377 Phage protein SAOUHSC_02184 phi PVL orf 14-like protein none 94.41 11.86 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=94.41; coverage=11.86 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(2048927..2049373) matched_representative_sequence=group_3377 AGNJKP_02328;BBHJIH_02178;CKFMFB_01093;DBPPGI_02545;DHHPLE_02175;DPEBLA_01912;EAMBND_02515;EDBMEK_02487;EFOOKO_02546;FHJCBG_02260;FHPENM_01806;FMOEEE_02668;GGEFGC_02550;GHNMBF_02148;GNKNJO_02599;HBKHOP_02188;HFICCC_03507;HGAGGM_02645;HJGKNO_02375;ILJMML_02542;JHLLHD_02040;JPKDEA_02071;KOFDAJ_02488;LPHLDL_02192;MGNIJD_02510;NBILEO_02513;NCJOOM_02791;NJAOBP_03648;NPGDHH_02376;OAHHLH_04855 phi PVL orf 14-like protein
87 group_2821 gene_presence_absence group_2821 group_2821 | SAOUHSC_02186 | none confidence group_2821 DUF806 domain-containing protein SAOUHSC_02186 phi PVL orf 12-like protein none 87.66 19.69 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=87.66; coverage=19.69 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(2050392..2050772) matched_representative_sequence=group_2821 AGNJKP_02330;BBHJIH_02176;CKFMFB_01091;DBPPGI_02547;DHHPLE_02173;DPEBLA_01910;EAMBND_02517;EDBMEK_02489;EFOOKO_02544;FHJCBG_02262;FHPENM_01804;FMOEEE_02666;GGEFGC_02548;GHNMBF_02150;GNKNJO_02597;HBKHOP_02190;HFICCC_03509;HGAGGM_02643;HJGKNO_02377;ILJMML_02540;JHLLHD_02042;JPKDEA_02073;KOFDAJ_02490;LPHLDL_02194;MGNIJD_02512;NBILEO_02515;NCJOOM_02759;NJAOBP_03646;NPGDHH_02378;OAHHLH_04857 phi PVL orf 12-like protein
88 group_2329 gene_presence_absence SAOUHSC_02200 (group_2329) group_2329 | SAOUHSC_02200 | high confidence group_2329 Phage protein SAOUHSC_02200 hypothetical protein high 97.21 93.98 High-confidence locus-level GenBank rescue. identity=97.21; coverage=93.98 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(2058606..2059076) matched_representative_sequence=group_2329 AGNJKP_02343;BBHJIH_02163;CKFMFB_01078;DBPPGI_02560;DHHPLE_02160;DPEBLA_01897;EAMBND_02530;EDBMEK_02502;EFOOKO_02531;FHJCBG_02275;FHPENM_01791;FMOEEE_02653;GGEFGC_02535;GHNMBF_02163;GNKNJO_02584;HBKHOP_02203;HFICCC_03522;HGAGGM_02630;HJGKNO_02390;ILJMML_02527;JHLLHD_02055;JPKDEA_02086;KOFDAJ_02503;LPHLDL_02207;MGNIJD_02525;NBILEO_02528;NCJOOM_02777;NJAOBP_03633;NPGDHH_02391;OAHHLH_04870 hypothetical protein
89 group_2300 gene_presence_absence yajD group_2300 | SAOUHSC_02198 | none confidence yajD Putative HNH nuclease YajD SAOUHSC_02198 hypothetical protein none 96.42 26.84 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=96.42; coverage=26.84 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(2057679..2058023) matched_representative_sequence=group_2300 AGNJKP_02341;BBHJIH_02165;CKFMFB_01080;DBPPGI_02558;DHHPLE_02162;DPEBLA_01899;EAMBND_02528;EDBMEK_02500;EFOOKO_02533;FHJCBG_02273;FHPENM_01793;FMOEEE_02655;GGEFGC_02537;GHNMBF_02161;GNKNJO_02586;HBKHOP_02201;HFICCC_03520;HGAGGM_02632;HJGKNO_02388;ILJMML_02529;JHLLHD_02053;JPKDEA_02084;KOFDAJ_02501;LPHLDL_02205;MGNIJD_02523;NBILEO_02526;NCJOOM_02805;NJAOBP_03635;NPGDHH_02389;OAHHLH_04868 hypothetical protein
90 group_1218 gene_presence_absence SAOUHSC_02196-like (group_1218) group_1218 | SAOUHSC_02196 | medium confidence group_1218 hypothetical protein;Terminase large subunit SAOUHSC_02196 phage terminase large subunit medium 99.94 65.19 Medium-confidence locus-level GenBank rescue. identity=99.94; coverage=65.19 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(2055385..2057079) matched_representative_sequence=group_1218 AGNJKP_02339;BBHJIH_02167;CKFMFB_01082;DBPPGI_02556;DHHPLE_02164;DPEBLA_01901;EAMBND_02526;EDBMEK_02498;EFOOKO_02535;FHJCBG_02271;FHPENM_01795;FMOEEE_02657;GGEFGC_02539;GHNMBF_02159;GNKNJO_02588;HBKHOP_02199;HFICCC_03518;HGAGGM_02634;HJGKNO_02386;ILJMML_02531;JHLLHD_02051;JPKDEA_02082;KOFDAJ_02499;LPHLDL_02203;MGNIJD_02521;NBILEO_02524;NCJOOM_02773;NJAOBP_03637;NPGDHH_02387;OAHHLH_04866 phage terminase large subunit
91 group_1183 gene_presence_absence SAOUHSC_02191-like (group_1183) group_1183 | SAOUHSC_02191 | medium confidence group_1183 HK97 family phage major capsid protein SAOUHSC_02191 HK97 family phage major capsid protein medium 99.84 79.57 Medium-confidence locus-level GenBank rescue. identity=99.84; coverage=79.57 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(2052003..2053250) matched_representative_sequence=group_1183 AGNJKP_02335;BBHJIH_02171;CKFMFB_01086;DBPPGI_02552;DHHPLE_02168;DPEBLA_01905;EAMBND_02522;EDBMEK_02494;EFOOKO_02539;FHJCBG_02267;FHPENM_01799;FMOEEE_02661;GGEFGC_02543;GHNMBF_02155;GNKNJO_02592;HBKHOP_02195;HFICCC_03514;HGAGGM_02638;HJGKNO_02382;ILJMML_02535;JHLLHD_02047;JPKDEA_02078;KOFDAJ_02495;LPHLDL_02199;MGNIJD_02517;NBILEO_02520;NCJOOM_02764;NJAOBP_03641;NPGDHH_02383;OAHHLH_04862 HK97 family phage major capsid protein
92 group_1090 gene_presence_absence group_1090 group_1090 | SAOUHSC_00181 | none confidence group_1090 hypothetical protein;HK97 gp10 family phage protein SAOUHSC_00181 hypothetical protein none 71.62 1.75 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=71.62; coverage=1.75 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity 198254..199222 matched_representative_sequence=group_10908 AGNJKP_02331;BBHJIH_02175;CKFMFB_01090;DBPPGI_02548;DHHPLE_02172;DPEBLA_01909;EAMBND_02518;EDBMEK_02490;EFOOKO_02543;FHJCBG_02263;FHPENM_01803;FMOEEE_02665;GGEFGC_02547;GHNMBF_02151;GNKNJO_02596;HBKHOP_02191;HFICCC_03510;HGAGGM_02642;HJGKNO_02378;ILJMML_02539;JHLLHD_02043;JPKDEA_02074;KOFDAJ_02491;LPHLDL_02195;MGNIJD_02513;NBILEO_02516;NCJOOM_02760;NJAOBP_03645;NPGDHH_02379;OAHHLH_04858 hypothetical protein
93 group_1014 gene_presence_absence group_1014 group_1014 | SAOUHSC_02916 | none confidence group_1014 Portal protein SAOUHSC_02916 aspartate alpha-decarboxylase none 75.13 5.99 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=75.13; coverage=5.99 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(2682298..2682669) matched_representative_sequence=group_10149 AGNJKP_02337;BBHJIH_02169;CKFMFB_01084;DBPPGI_02554;DHHPLE_02166;DPEBLA_01903;EAMBND_02524;EDBMEK_02496;EFOOKO_02537;FHJCBG_02269;FHPENM_01797;FMOEEE_02659;GGEFGC_02541;GHNMBF_02157;GNKNJO_02590;HBKHOP_02197;HFICCC_03516;HGAGGM_02636;HJGKNO_02384;ILJMML_02533;JHLLHD_02049;JPKDEA_02080;KOFDAJ_02497;LPHLDL_02201;MGNIJD_02519;NBILEO_02522;NCJOOM_02771;NJAOBP_03639;NPGDHH_02385;OAHHLH_04864 aspartate alpha-decarboxylase
94 group_680 gene_presence_absence group_680 group_680 | SAOUHSC_00688 | none confidence group_680 DUF1056 domain-containing protein SAOUHSC_00688 hypothetical protein none 76.19 4.59 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=76.19; coverage=4.59 29 50 0.5800 4 50 0.0800 cases (MRSA) 2.46 14.1783 4.645-43.28 4.64515 43.2761 3.48e-06 12.2840 Panaroo/Bakta+GenBank nucleotide_similarity complement(672925..673491) matched_representative_sequence=group_6805 AGNJKP_02338;BBHJIH_02168;CKFMFB_01083;DBPPGI_02555;DHHPLE_02165;DPEBLA_01902;EAMBND_02525;EDBMEK_02497;EFOOKO_02536;FHJCBG_02270;FHPENM_01796;FMOEEE_02658;GGEFGC_02540;GHNMBF_02158;GNKNJO_02589;HBKHOP_02198;HFICCC_03517;HGAGGM_02635;HJGKNO_02385;ILJMML_02532;JHLLHD_02050;JPKDEA_02081;KOFDAJ_02498;LPHLDL_02202;MGNIJD_02520;NBILEO_02523;NCJOOM_02772;NJAOBP_03638;NPGDHH_02386;OAHHLH_04865 hypothetical protein
95 group_6870 gene_presence_absence SAOUHSC_02220-like (group_6870) group_6870 | SAOUHSC_02220 | medium confidence group_6870 Single-stranded DNA-binding protein SAOUHSC_02220 phi ETA orf 18-like protein medium 99.64 63.59 Medium-confidence locus-level GenBank rescue. identity=99.64; coverage=63.59 14 50 0.2800 0 50 0.0000 cases (MRSA) 3.35 40.1233 2.318-694.5 2.31807 694.49 0.000116 12.2619 Panaroo/Bakta+GenBank nucleotide_similarity complement(2065949..2066500) matched_representative_sequence=group_6870 BCINDJ_02231;DBPPGI_02470;DGCAMH_02745;EBFKMK_02745;EFOOKO_02468;GGEFGC_02441;GGOGND_02606;GNKNJO_02371;GNNCOP_01029;HJFIGM_01999;NCJOOM_02790;PBDKDP_02074;PHCLFM_02506;PJCLAL_00875 phi ETA orf 18-like protein
96 group_5172 gene_presence_absence SAOUHSC_00047-like (group_5172) group_5172 | SAOUHSC_00047 | low confidence group_5172 DUF5079 domain-containing protein;hypothetical protein SAOUHSC_00047 hypothetical protein low 96.79 41.67 Low-confidence locus-level GenBank rescue. identity=96.79; coverage=41.67 50 50 1.0000 29 50 0.5800 cases (MRSA) 10.7 73.6102 4.299-1260 4.29877 1260.47 0.000951 12.2237 Panaroo/Bakta+GenBank nucleotide_similarity 49490..50092 matched_representative_sequence=group_5172 AAFANJ_01617;ADDHAP_01059;AGNJKP_00371;BBHJIH_02404;BCINDJ_00967;BGHJOB_01317;BLNHMO_00876;CCGLPJ_01155;CDDCHJ_01698;CIALCM_00191;CJJPLC_00264;CNMMKL_01216;DBPPGI_00773;DGCAMH_01192;DHHPLE_02418;DNJFEH_00881;DPEBLA_02237;EAMBND_02511;EBFKMK_01350;EBHIAF_00748;EDBMEK_00465;EEPHOB_00282;EFOOKO_00491;EOFOFH_01190;FCNEHE_00879;FDFIHM_00939;FHJCBG_01093;FHPENM_00898;FIIBJA_01001;FJPBEI_03077 hypothetical protein
97 set26 gene_presence_absence ;set26 set26 | SAOUHSC_00399 | none confidence ;set26 Superantigen-like protein 11;superantigen-like protein SSL11;hypothetical protein SAOUHSC_00399 superantigen-like protein none 57.54 8.55 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=57.54; coverage=8.55 49 50 0.9800 24 50 0.4800 cases (MRSA) 2.84 35.6939 6.425-198.3 6.42507 198.294 9.39e-05 12.1849 Panaroo/Bakta+GenBank nucleotide_similarity 402508..403185 matched_representative_sequence=set26 AAFANJ_01294;ADDHAP_01159;AGNJKP_00697;BBHJIH_02499;BCINDJ_02664;BGHJOB_02673;CCGLPJ_01480;CDDCHJ_01621;CKFMFB_02202;CNMMKL_02109;DBPPGI_00447;DGCAMH_00867;DHHPLE_02533;DPEBLA_00467;EAMBND_01298;EBFKMK_01025;EBHIAF_02547;EBHIAF_02548;EDBMEK_00791;EEPHOB_02297;EFOOKO_00817;EOFOFH_00863;FCNEHE_01331;FHPENM_00571;FIIBJA_01324;FJPBEI_03080;FMAEJP_02349;FMOEEE_02006;GEIAPO_02221;GGEFGC_00447 superantigen-like protein
98 group_2734 gene_presence_absence group_2734 group_2734 | SAOUHSC_02795 | none confidence group_2734 DUF3784 domain-containing protein SAOUHSC_02795 hypothetical protein none 83.82 12.94 No confident reference gene assignment; report the stable Panaroo cluster ID. identity=83.82; coverage=12.94 49 50 0.9800 24 50 0.4800 cases (MRSA) 2.84 35.6939 6.425-198.3 6.42507 198.294 9.49e-05 12.1803 Panaroo/Bakta+GenBank nucleotide_similarity 2567802..2568110 matched_representative_sequence=group_2734 AAFANJ_01925;ADDHAP_01448;AGNJKP_00079;BBHJIH_01448;BCINDJ_01612;BGHJOB_01949;CCGLPJ_01950;CDDCHJ_00695;CKFMFB_00272;CNMMKL_00616;DBPPGI_01666;DGCAMH_01480;DHHPLE_01446;DPEBLA_01734;EAMBND_02070;EBFKMK_01589;EBHIAF_01815;EDBMEK_01829;EEPHOB_02440;EFOOKO_01934;EOFOFH_01717;FCNEHE_00596;FHJCBG_01356;FHPENM_02456;FIIBJA_01674;FJPBEI_02807;FMAEJP_00809;FMOEEE_01463;GEIAPO_01031;GGEFGC_01635 hypothetical protein
99 sep~~~sea gene_presence_absence ;sep;sea sep~~~sea | SAOUHSC_00009 | none confidence ;sep;sea Enterotoxin type A;staphylococcal enterotoxin type P;staphylococcal enterotoxin type A SAOUHSC_00009 seryl-tRNA synthetase none 34.59 1.66 Displayed from Panaroo/Bakta annotation; no stronger GenBank rescue available. identity=34.59; coverage=1.66 22 50 0.4400 2 50 0.0400 cases (MRSA) 2.84 15.3158 3.83-61.25 3.82955 61.2536 7.08e-06 12.0869 Panaroo/Bakta+GenBank nucleotide_similarity 12786..14072 matched_representative_sequence=sep~~~sea AAFANJ_02743;BCINDJ_02189;DBPPGI_02538;DPEBLA_01919;EDBMEK_02480;EFOOKO_02553;FHPENM_01813;FIIBJA_02009;FJPBEI_01727;FMOEEE_02703;GGEFGC_02557;GHNMBF_02141;GNNCOP_01442;HFCIAM_02326;HFICCC_04023;HJFIGM_02041;HJGKNO_02368;HLEGMA_02301;ILJMML_02549;NJAOBP_03481;NMHDHA_02339;PBDKDP_02032;PHCLFM_02223;PKFOMJ_01696 seryl-tRNA synthetase
100 group_557 gene_presence_absence SAOUHSC_01258 (group_557) group_557 | SAOUHSC_01258 | high confidence group_557 hypothetical protein SAOUHSC_01258 hypothetical protein high 100.00 100.00 High-confidence locus-level GenBank rescue. identity=100.00; coverage=100.00 38 50 0.7600 10 50 0.2000 cases (MRSA) 2.17 11.88 4.68-30.16 4.67992 30.1574 4.49e-06 11.9182 Panaroo/Bakta+GenBank nucleotide_exact_or_contained 1212830..1213657 matched_representative_sequence=group_5575 39_refound_179_pseudo;49_refound_342_pseudo;AAFANJ_02600;AGNJKP_02364;BBHJIH_02141;CNMMKL_00100;DBPPGI_02332;DHHPLE_02138;DPEBLA_01884;EAMBND_02597;EDBMEK_02521;EFOOKO_02379;FCNEHE_02080;FHJCBG_02293;FHPENM_01772;FIIBJA_02046;FJPBEI_01585;FMAEJP_02034;FMOEEE_00557;GEIAPO_02538;GGEFGC_02302;GHNMBF_02183;GNKNJO_02644;HBKHOP_02225;HFCIAM_02363;HFICCC_03943;HGAGGM_02708;HJGKNO_02409;HLEGMA_02338;IGAMFP_02121 hypothetical protein

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09 Reference annotation confidence guide

Brief interpretation: The confidence guide explains how reference annotation rescue should be interpreted. Low-confidence or unmatched markers should retain their stable Panaroo/SNP identifiers.
Annotation caveat: Reference annotation rescue is intended to improve interpretability of pangenome/SNP markers. Low-confidence matches should not be treated as definitive gene calls. Candidate hits should be validated in independent datasets and interpreted in the context of case (MRSA) versus control (MSSA).
ConfidenceRuleInterpretation
high>=95% identity and >=90% coverage, or exact qualifier-level supportStrong reference-supported annotation
medium>=85% identity and >=70% coveragePlausible annotation; inspect manually
low>=60% identity and >=50% coverage, or weak/partial supportTentative annotation only
noneNo usable GenBank matchKeep the pangenome/SNP marker identifier

Reference annotation summary

metric	value
reference_cds_parsed	2767
reference_parse_warning	
panaroo_clusters_parsed	12795
annotation_engine	Panaroo/Bakta
fasta_records_parsed	281523
top_priority_input	rMAP_GWAS_top_priority_hits.tsv
all_significant_input	rMAP_GWAS_all_significant_hits.tsv
method	GenBank qualifier matching plus pure-Python nucleotide similarity rescue when Panaroo representative sequences are available
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10 Input validation

Brief interpretation: The validation report checks input consistency, sample counts, paired FASTQ arrays, and phenotype coding before downstream interpretation.
rMAP-GWAS sample-set input validation report
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Cases (MRSA): 50
Controls (MSSA): 50
Total samples: 100
Case (MRSA) label: case (MRSA)
Control (MSSA) label: control (MSSA)
Phenotype display metadata values provided: yes
Unique phenotype display values: MRSA, MSSA

Status: PASS
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11 Panaroo summary

Brief interpretation: The Panaroo summary describes the pangenome graph and gene matrix generated from Bakta-derived GFF files.
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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12 Interpretation guidance

Brief interpretation: These notes summarize major microbial GWAS caveats, including population structure, recombination, small sample size, and phenotype misclassification.
Microbial GWAS can be confounded by lineage structure, outbreak clustering, recombination, phenotype misclassification, small sample size, species background, variable sequencing depth/assembly quality, point mutations outside gene presence/absence, and co-carriage of multiple resistance genes in the same antibiotic class. Use the population-structure plots, QC outputs, optional SNP GWAS, and, for recombining species, consider enabling Gubbins to reduce recombinant-block-driven SNP associations. Interpret candidate markers as associations with case (MRSA) versus control (MSSA), not as proven causal determinants or standalone clinical resistance calls.
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13 Key output files

Brief interpretation: This section records the key files needed for review, reruns, sharing, and downstream manuscript or supplementary reporting.

Click any output card to download the file. The cards are kept inside one responsive frame, so this section should not require horizontal scrolling.

PhenotyperMAP_GWAS_phenotype_legend.tsvMetadata-derived legend used throughout this report.Download GWASpyseer_gene_assoc.tsvRaw pyseer gene association results. Rows detected: 12794.Download SNP GWASpyseer_snp_assoc.tsvRaw pyseer SNP marker association results. Rows detected: 3050.Download PriorityrMAP_GWAS_top_priority_hits.annotated.tsvRanked top gene hits with reference annotation columns.Download Structuremash_distances.tsvSquare Mash distance matrix used for correction and visualization.Download
rMAP-GWAS report generated from successful Cromwell workflow outputs.