Samples analyzed10
Top species groups3
Total AMR hits8
Median N5047,634
1. Executive summary
The primary detected fungal species group was Candida albicans. The sample-level cards below provide a compact interpretation of species assignment, QUAST assembly-contiguity metrics, phylogeny status, and genomic AMR screening status.
Interpretation note: genomic antifungal-resistance findings should be treated as screening evidence. Clinically important results should be interpreted with isolate metadata, species identity, validated mutation catalogues, and phenotypic antifungal susceptibility testing where required.
Species distribution
Candida albicans8
Candida parapsilosis1
Candida tropicalis1
2. Surveillance readiness and interpretation dashboard
This integrated table combines species confidence, QUAST assembly-contiguity metrics, AMR marker status, phylogeny eligibility, and optional metadata into a practical surveillance-readiness view.
| Sample | Collection date | site | species | Species confidence | Assembly QC | QUAST contiguity QC | AMR screen | Phylogeny | Surveillance status | Reason / note |
|---|---|---|---|---|---|---|---|---|---|---|
| SRR30894123 | 2021-10 | Mbarara | Candida albicans | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR30894124 | 2021-10 | Mbarara | Candida albicans | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR30894128 | 2021-10 | Mbarara | Candida albicans | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR30894135 | 2021-10 | Mbarara | Candida albicans | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR30894139 | 2021-10 | Mbarara | Candida albicans | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR33417537 | 2023-08-16 | Kampala | Candida albicans | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR33417538 | 2023-08-16 | Kampala | Candida albicans | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR33417539 | 2023-08-16 | Kampala | Candida parapsilosis | High | Pass | Pass | No curated marker detected | Excluded | Ready for surveillance interpretation | No major automated warning flags using species typing, QUAST assembly QC, AMR screening, and phylogeny status |
| SRR33417540 | 2022-06-22 | Kampala | Candida albicans | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR33417542 | 2019-03-14 | Kampala | Candida tropicalis | High | Review | Review | No curated marker detected | Excluded | Review | QUAST assembly QC |
3. Surveillance metadata
| Sample | country | site | collection_date | specimen_type | patient_group | ward_or_facility | sequencing_platform |
|---|---|---|---|---|---|---|---|
| SRR33417539 | Uganda | Kampala | 2023-08-16 | blood | human | Kampala | ILLUMINA; Illumina HiSeq 2000 |
| SRR33417540 | Uganda | Kampala | 2022-06-22 | blood | human | Kampala | ILLUMINA; Illumina HiSeq 2000 |
| SRR33417542 | Uganda | Kampala | 2019-03-14 | blood | human | Kampala | ILLUMINA; Illumina HiSeq 2000 |
| SRR33417537 | Uganda | Kampala | 2023-08-16 | blood | human | Kampala | ILLUMINA; Illumina HiSeq 2000 |
| SRR33417538 | Uganda | Kampala | 2023-08-16 | blood | human | Kampala | ILLUMINA; Illumina HiSeq 2000 |
| SRR30894123 | Uganda | Mbarara | 2021-10 | blood | human | Mbarara | ILLUMINA; NextSeq 500 |
| SRR30894128 | Uganda | Mbarara | 2021-10 | blood | human | Mbarara | ILLUMINA; NextSeq 500 |
| SRR30894135 | Uganda | Mbarara | 2021-10 | blood | human | Mbarara | ILLUMINA; NextSeq 500 |
| SRR30894139 | Uganda | Mbarara | 2021-10 | blood | human | Mbarara | ILLUMINA; NextSeq 500 |
| SRR30894124 | Uganda | Mbarara | 2021-10 | blood | human | Mbarara | ILLUMINA; NextSeq 500 |
4. Sample-level surveillance summary
SRR30894123
Candida albicans Review
Species reads99.21%
Contigs1,506
N5033,842
GC (%)33.42
1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible
Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (8 samples)
SRR30894124
Candida albicans Review
Species reads99.54%
Contigs1,237
N5052,568
GC (%)33.43
1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible
Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (8 samples)
SRR30894128
Candida albicans Review
Species reads99.36%
Contigs1,603
N5042,869
GC (%)33.42
1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible
Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (8 samples)
SRR30894135
Candida albicans Review
Species reads99.09%
Contigs1,382
N5037,919
GC (%)33.39
1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible
Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (8 samples)
SRR30894139
Candida albicans Review
Species reads98.56%
Contigs1,586
N5040,477
GC (%)33.41
1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible
Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (8 samples)
SRR33417537
Candida albicans Review
Species reads99.37%
Contigs1,354
N5052,873
GC (%)33.40
1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible
Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (8 samples)
SRR33417538
Candida albicans Review
Species reads99.52%
Contigs1,143
N5058,607
GC (%)33.37
1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible
Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (8 samples)
SRR33417539
Candida parapsilosis Ready for surveillance interpretation
Species reads100.00%
Contigs366
N50118,140
GC (%)38.65
No curated genomic AMR marker detected — not susceptible Species confidence: High Phylogeny: Excluded
Interpretation: No major automated warning flags using species typing, QUAST assembly QC, AMR screening, and phylogeny status. Species note: Top species abundance ≥95%. Phylogeny note: Skipped by rc172 phylogeny guard because this detected species is not among the defined Candida species with an exported reference FASTA. Valid species with references are still processed.
SRR33417540
Candida albicans Review
Species reads99.41%
Contigs1,270
N5052,398
GC (%)33.40
1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible
Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (8 samples)
SRR33417542
Candida tropicalis Review
Species reads99.84%
Contigs6,414
N507,269
GC (%)33.23
No curated genomic AMR marker detected — not susceptible Species confidence: High Phylogeny: Excluded
Interpretation: QUAST assembly QC. Species note: Top species abundance ≥95%. Phylogeny note: Requires at least 3 samples for a species-specific tree.
5. Candida species typing using Kraken2/Bracken
Top species calls are derived from the custom Candida-focused Kraken2/Bracken database bundled in the species-typing Docker image.
| Sample | Top species | Reads (%) | clade_reads | taxon_reads | taxid | evidence |
|---|---|---|---|---|---|---|
| SRR30894123 | Candida albicans | 99.21% | 1,047,352 | 1,047,352 | 5476 | Bracken species-level abundance |
| SRR30894124 | Candida albicans | 99.54% | 4,937,408 | 4,937,408 | 5476 | Bracken species-level abundance |
| SRR30894128 | Candida albicans | 99.36% | 1,385,339 | 1,385,339 | 5476 | Bracken species-level abundance |
| SRR30894135 | Candida albicans | 99.09% | 1,294,442 | 1,294,442 | 5476 | Bracken species-level abundance |
| SRR30894139 | Candida albicans | 98.56% | 1,898,169 | 1,898,169 | 5476 | Bracken species-level abundance |
| SRR33417537 | Candida albicans | 99.37% | 6,006,766 | 6,006,766 | 5476 | Bracken species-level abundance |
| SRR33417538 | Candida albicans | 99.52% | 5,076,219 | 5,076,219 | 5476 | Bracken species-level abundance |
| SRR33417539 | Candida parapsilosis | 100.00% | 5,428,052 | 5,428,052 | 5480 | Bracken species-level abundance |
| SRR33417540 | Candida albicans | 99.41% | 5,113,114 | 5,113,114 | 5476 | Bracken species-level abundance |
| SRR33417542 | Candida tropicalis | 99.84% | 4,165,855 | 4,165,855 | 5482 | Bracken species-level abundance |
6. MEGAHIT assembly summary
| Sample | contigs | Total bp | N50 | Largest contig |
|---|---|---|---|---|
| SRR30894123 | 1,506 | 14,718,384 | 33,842 | 182,321 |
| SRR30894124 | 1,237 | 14,709,483 | 52,568 | 255,210 |
| SRR30894128 | 1,603 | 14,868,931 | 42,869 | 190,964 |
| SRR30894135 | 1,382 | 14,676,400 | 37,919 | 169,037 |
| SRR30894139 | 1,586 | 14,895,586 | 40,477 | 238,813 |
| SRR33417537 | 1,354 | 14,797,663 | 52,873 | 275,261 |
| SRR33417538 | 1,143 | 14,605,241 | 58,607 | 307,598 |
| SRR33417539 | 366 | 12,897,863 | 118,140 | 473,263 |
| SRR33417540 | 1,270 | 14,771,182 | 52,398 | 377,705 |
| SRR33417542 | 6,414 | 27,931,208 | 7,269 | 135,959 |
7. Assembly quality assessment with QUAST
QUAST values are parsed from the native per-sample report.tsv format and transposed into one row per sample. This default surveillance mode reports QUAST assembly contiguity metrics such as contig count, total length, N50, largest contig, and GC percentage. It is very fast. BUSCO and Compleasm tasks are available as optional modules, but they are disabled by default in the recommended JSON and are not required for this QUAST-based assembly assessment.
| Sample | # contigs | Largest contig | Total length | GC (%) | N50 |
|---|---|---|---|---|---|
| SRR30894123 | 1,506 | 182,321 | 14,718,384 | 33.42 | 33,842 |
| SRR30894124 | 1,237 | 255,210 | 14,709,483 | 33.43 | 52,568 |
| SRR30894128 | 1,603 | 190,964 | 14,868,931 | 33.42 | 42,869 |
| SRR30894135 | 1,382 | 169,037 | 14,676,400 | 33.39 | 37,919 |
| SRR30894139 | 1,586 | 238,813 | 14,895,586 | 33.41 | 40,477 |
| SRR33417537 | 1,354 | 275,261 | 14,797,663 | 33.40 | 52,873 |
| SRR33417538 | 1,143 | 307,598 | 14,605,241 | 33.37 | 58,607 |
| SRR33417539 | 366 | 473,263 | 12,897,863 | 38.65 | 118,140 |
| SRR33417540 | 1,270 | 377,705 | 14,771,182 | 33.40 | 52,398 |
| SRR33417542 | 6,414 | 135,959 | 27,931,208 | 33.23 | 7,269 |
8. Fungal antifungal-resistance characterization
This section reports mutation/gene-level evidence emitted by the configured fungal AMR container. A “No marker detected” result is not a susceptible call. Fluconazole resistance can be caused by ERG11 alterations, TAC1/UPC2/MRR1/PDR1-mediated efflux, aneuploidy/LOH, copy-number changes, species-specific mechanisms, or markers absent from the current AMR database.
| Sample | species | drug_class | drug | Gene / status | mutation | effect | evidence_level | interpretation |
|---|---|---|---|---|---|---|---|---|
| SRR30894123 | Candida albicans | azole | fluconazole/other azoles | Cyp51 | E266D | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 E266D (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-1). Source: amr_out/SRR30894123.ChroQueTas/SRR30894123.contigs.ChroQueTaS.Cyp51.1.tsv:266 |
| SRR30894124 | Candida albicans | azole | fluconazole/other azoles | Mrr1 | E1020Q | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Mrr1 E1020Q (FungAMR MUTATION). Drug evidence from ChroQueTas: Brefeldin_A(NA/-1),Cerulenin(NA/-1),Fluconazole(NA/-1). Source: amr_out/SRR30894124.ChroQueTas/SRR30894124.contigs.ChroQueTaS.Mrr1.1.tsv:1020 |
| SRR30894128 | Candida albicans | azole | fluconazole/other azoles | Mrr1 | E1020Q | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Mrr1 E1020Q (FungAMR MUTATION). Drug evidence from ChroQueTas: Brefeldin_A(NA/-1),Cerulenin(NA/-1),Fluconazole(NA/-1). Source: amr_out/SRR30894128.ChroQueTas/SRR30894128.contigs.ChroQueTaS.Mrr1.1.tsv:1020 |
| SRR30894135 | Candida albicans | azole | fluconazole/other azoles | Cap1 | M140I | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cap1 M140I (FungAMR MUTATION). Drug evidence from ChroQueTas: Clotrimazole(3/NA),Fluconazole(3/NA),Fluconazole(NA/-1),Isavuconazole(3/NA),Itraconazole(3/NA),Itraconazole(NA/-1),Ketoconazole(NA/-1),Posaconazole(3/NA),Posaconazole(NA/-1),Voriconazole(3/NA),Voriconazole(NA/-1). Source: amr_out/SRR30894135.ChroQueTas/SRR30894135.contigs.ChroQueTaS.Cap1.1.tsv:140 |
| SRR30894139 | Candida albicans | azole | fluconazole/other azoles | Cyp51 | E266D | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 E266D (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-1). Source: amr_out/SRR30894139.ChroQueTas/SRR30894139.contigs.ChroQueTaS.Cyp51.1.tsv:266 |
| SRR33417537 | Candida albicans | azole | fluconazole/other azoles | Cyp51 | E266D | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 E266D (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-1). Source: amr_out/SRR33417537.ChroQueTas/SRR33417537.contigs.ChroQueTaS.Cyp51.1.tsv:266 |
| SRR33417538 | Candida albicans | azole | fluconazole/other azoles | Cyp51 | V437I | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 V437I (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(8/-2),Isavuconazole(8/NA),Itraconazole(8/-8),Posaconazole(8/NA),Voriconazole(8/-8). Source: amr_out/SRR33417538.ChroQueTas/SRR33417538.contigs.ChroQueTaS.Cyp51.1.tsv:437 |
| SRR33417539 | Candida parapsilosis | azole/other | fluconazole/other | No marker — not susceptible | NA | NA | scanner_detected_candidate_marker | The AMR scanner produced text consistent with a possible curated resistance marker, but rc151 could not parse an exact ChroQueTas marker row. Review fungal_amr.raw.tsv and fungal_amr.log for the exact record: amr_out/SRR33417539.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR33417539.contigs |
| SRR33417540 | Candida albicans | azole | fluconazole/other azoles | Cyp51 | E266D | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 E266D (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-1). Source: amr_out/SRR33417540.ChroQueTas/SRR33417540.contigs.ChroQueTaS.Cyp51.1.tsv:266 |
| SRR33417542 | Candida tropicalis | azole/other | fluconazole/other | No marker — not susceptible | NA | NA | scanner_detected_candidate_marker | The AMR scanner produced text consistent with a possible curated resistance marker, but rc151 could not parse an exact ChroQueTas marker row. Review fungal_amr.raw.tsv and fungal_amr.log for the exact record: amr_out/SRR33417542.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR33417542.contigs |
9. Species-aware core-SNP phylogeny
When enabled, rMAP-Candida builds phylogenies separately for each species with sufficient samples and a matching reference. Mixed-species phylogenies are intentionally avoided. Outputs include species-group summaries, core-SNP alignments, and IQ-TREE Newick trees.
| Species | Status | Samples | Variant-calling branch | Ploidy model | Core variable sites | Notes |
|---|---|---|---|---|---|---|
| Candida parapsilosis | SKIPPED_SPECIES_NOT_IN_REFERENCE_MANIFEST | 1 | NA | NA | NA | Skipped by rc172 phylogeny guard because this detected species is not among the defined Candida species with an exported reference FASTA. Valid species with references are still processed. |
| Candida albicans | PASS | 8 | snippy_core_rc170_tb_style | NA | 9295 | rc170 used the rMAP-TB-style Snippy -> snippy-core branch. Species grouping was based on Kraken2/Bracken top-species calls; mixed-species trees are intentionally avoided. Recombination is not explicitly filtered. |
| Candida tropicalis | SKIPPED_TOO_FEW_SAMPLES | 1 | snippy_core | 1 | NA | Requires at least 3 samples for a species-specific tree. |
Candida albicans
Species without a displayed tree:
- Candida parapsilosis: SKIPPED_SPECIES_NOT_IN_REFERENCE_MANIFEST; samples after species-specific consensus/eligibility = 1; branch = NA; note = Skipped by rc172 phylogeny guard because this detected species is not among the defined Candida species with an exported reference FASTA. Valid species with references are still processed.
- Candida tropicalis: SKIPPED_TOO_FEW_SAMPLES; samples after species-specific consensus/eligibility = 1; branch = snippy_core; note = Requires at least 3 samples for a species-specific tree.
Phylogeny interpretation note: rMAP-Candida builds one tree per species. Mixed-species Candida phylogenies are intentionally avoided. Treat these trees as species-level genomic relatedness visualizations unless recombination filtering and epidemiologic metadata support transmission interpretation.
10. Species-aware pairwise SNP distances and closest-neighbor summary
Closest-neighbor summary
| species | Sample | Closest sample | SNP distance | Conservative cluster flag |
|---|---|---|---|---|
| Candida albicans | SRR30894123 | SRR33417540 | 368 | Distinct / review with metadata |
| Candida albicans | SRR30894124 | SRR30894123 | 986 | Distinct / review with metadata |
| Candida albicans | SRR30894128 | SRR30894123 | 1013 | Distinct / review with metadata |
| Candida albicans | SRR30894135 | SRR30894128 | 2585 | Distinct / review with metadata |
| Candida albicans | SRR30894139 | SRR33417537 | 650 | Distinct / review with metadata |
| Candida albicans | SRR33417537 | SRR30894139 | 650 | Distinct / review with metadata |
| Candida albicans | SRR33417538 | SRR30894128 | 4406 | Distinct / review with metadata |
| Candida albicans | SRR33417540 | SRR30894123 | 368 | Distinct / review with metadata |
Pairwise SNP-distance matrix/table
| species | Sample A | Sample B | SNP distance | Compared core-SNP sites |
|---|---|---|---|---|
| Candida albicans | SRR30894123 | SRR30894124 | 986 | 9295 |
| Candida albicans | SRR30894123 | SRR30894128 | 1013 | 9295 |
| Candida albicans | SRR30894123 | SRR30894135 | 2835 | 9295 |
| Candida albicans | SRR30894123 | SRR30894139 | 1921 | 9295 |
| Candida albicans | SRR30894123 | SRR33417537 | 2157 | 9295 |
| Candida albicans | SRR30894123 | SRR33417538 | 4659 | 9295 |
| Candida albicans | SRR30894123 | SRR33417540 | 368 | 9295 |
| Candida albicans | SRR30894124 | SRR30894128 | 1014 | 9295 |
| Candida albicans | SRR30894124 | SRR30894135 | 2894 | 9295 |
| Candida albicans | SRR30894124 | SRR30894139 | 2024 | 9295 |
| Candida albicans | SRR30894124 | SRR33417537 | 2294 | 9295 |
| Candida albicans | SRR30894124 | SRR33417538 | 4753 | 9295 |
| Candida albicans | SRR30894124 | SRR33417540 | 1206 | 9295 |
| Candida albicans | SRR30894128 | SRR30894135 | 2585 | 9295 |
| Candida albicans | SRR30894128 | SRR30894139 | 1694 | 9295 |
| Candida albicans | SRR30894128 | SRR33417537 | 1924 | 9295 |
| Candida albicans | SRR30894128 | SRR33417538 | 4406 | 9295 |
| Candida albicans | SRR30894128 | SRR33417540 | 1201 | 9295 |
| Candida albicans | SRR30894135 | SRR30894139 | 3299 | 9295 |
| Candida albicans | SRR30894135 | SRR33417537 | 3243 | 9295 |
| Candida albicans | SRR30894135 | SRR33417538 | 5346 | 9295 |
| Candida albicans | SRR30894135 | SRR33417540 | 3063 | 9295 |
| Candida albicans | SRR30894139 | SRR33417537 | 650 | 9295 |
| Candida albicans | SRR30894139 | SRR33417538 | 5017 | 9295 |
| Candida albicans | SRR30894139 | SRR33417540 | 2127 | 9295 |
| Candida albicans | SRR33417537 | SRR33417538 | 4869 | 9295 |
| Candida albicans | SRR33417537 | SRR33417540 | 2389 | 9295 |
| Candida albicans | SRR33417538 | SRR33417540 | 4823 | 9295 |
SNP-distance interpretation: low SNP distances suggest close genetic relatedness but should not be interpreted as transmission without epidemiological metadata, recombination-aware analysis, and species-specific validation.
11. Output navigation and provenance
The workflow emits downloadable tabular outputs in addition to this integrated HTML report.
rMAP-Myc-Candida-Candida_summary.tsv
rMAP_Candida_surveillance_summary.tsv
rMAP_Candida_pairwise_snp_distances.tsv
- Per-sample Kraken2, Bracken, FASTQ QC, assembly, QUAST, AMR, and optional phylogeny files are available in the Cromwell execution outputs.
- Dockerized execution supports reproducibility across local Cromwell and cloud environments.