Samples analyzed17
Top species groups4
Total AMR hits13
Median N5029,270
1. Executive summary
The primary detected fungal species group was Candidozyma auris. 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
Candidozyma auris12
Candida parapsilosis3
Candida albicans1
Nakaseomyces glabratus1
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 |
|---|---|---|---|---|---|---|---|---|---|---|
| ERR263534 | NA | NA | Candida albicans | High | Pass | Pass | 1 marker(s) | Excluded | Review | AMR marker detected |
| ERR331060 | NA | NA | Nakaseomyces glabratus | Low / review | Pass | Pass | No curated marker detected | Excluded | Review | species confidence |
| SRR25474571 | NA | NA | 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 |
| SRR25474602 | NA | NA | 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 |
| SRR25474605 | NA | NA | 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 |
| SRR38463714 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38463716 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38770855 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38770856 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38770857 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38770858 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38770859 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38770860 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38770861 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38770862 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38770863 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38770864 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
3. Surveillance metadata
No surveillance metadata TSV was provided. Add
rMAP_Candida.surveillance_metadata_tsv to your input JSON to display collection date, country/site, specimen type, patient group, facility/ward, and sequencing platform.4. Sample-level surveillance summary
ERR263534
Candida albicans Review
Species reads99.62%
Contigs1,234
N5057,289
GC (%)33.43
1 AMR hit(s) Species confidence: High Phylogeny: Excluded
Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Requires at least 3 samples for a species-specific tree.
ERR331060
Nakaseomyces glabratus Review
Species reads73.73%
Contigs427
N5067,770
GC (%)38.08
No curated genomic AMR marker detected — not susceptible Species confidence: Low / review Phylogeny: Excluded
Interpretation: species confidence. Species note: Top species abundance <80%; possible mixed sample, contamination, or weak species assignment. Phylogeny note: Requires at least 3 samples for a species-specific tree.
SRR25474571
Candida parapsilosis Ready for surveillance interpretation
Species reads100.00%
Contigs853
N5033,626
GC (%)38.63
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.
SRR25474602
Candida parapsilosis Ready for surveillance interpretation
Species reads99.99%
Contigs951
N5028,822
GC (%)38.61
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.
SRR25474605
Candida parapsilosis Ready for surveillance interpretation
Species reads99.96%
Contigs1,070
N5024,883
GC (%)38.61
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.
SRR38463714
Candidozyma auris Review
Species reads99.22%
Contigs126
N50187,990
GC (%)45.14
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 (12 samples)
SRR38463716
Candidozyma auris Review
Species reads99.45%
Contigs130
N50254,478
GC (%)45.14
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 (12 samples)
SRR38770855
Candidozyma auris Review
Species reads99.53%
Contigs812
N5029,270
GC (%)44.94
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 (12 samples)
SRR38770856
Candidozyma auris Review
Species reads99.41%
Contigs737
N5030,299
GC (%)44.94
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 (12 samples)
SRR38770857
Candidozyma auris Review
Species reads99.64%
Contigs797
N5029,892
GC (%)44.92
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 (12 samples)
SRR38770858
Candidozyma auris Review
Species reads99.58%
Contigs819
N5029,237
GC (%)44.92
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 (12 samples)
SRR38770859
Candidozyma auris Review
Species reads99.75%
Contigs838
N5025,695
GC (%)44.92
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 (12 samples)
SRR38770860
Candidozyma auris Review
Species reads99.00%
Contigs820
N5028,474
GC (%)44.92
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 (12 samples)
SRR38770861
Candidozyma auris Review
Species reads99.64%
Contigs794
N5028,263
GC (%)44.92
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 (12 samples)
SRR38770862
Candidozyma auris Review
Species reads99.18%
Contigs840
N5027,503
GC (%)44.93
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 (12 samples)
SRR38770863
Candidozyma auris Review
Species reads99.70%
Contigs747
N5032,589
GC (%)44.92
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 (12 samples)
SRR38770864
Candidozyma auris Review
Species reads99.34%
Contigs852
N5027,621
GC (%)44.90
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 (12 samples)
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 |
|---|---|---|---|---|---|---|
| ERR263534 | Candida albicans | 99.62% | 2,597,066 | 2,597,066 | 5476 | Bracken species-level abundance |
| ERR331060 | Nakaseomyces glabratus | 73.73% | 190,301 | 190,301 | 5478 | Bracken species-level abundance |
| SRR25474571 | Candida parapsilosis | 100.00% | 2,251,869 | 2,251,869 | 5480 | Bracken species-level abundance |
| SRR25474602 | Candida parapsilosis | 99.99% | 2,338,068 | 2,338,068 | 5480 | Bracken species-level abundance |
| SRR25474605 | Candida parapsilosis | 99.96% | 2,409,486 | 2,409,486 | 5480 | Bracken species-level abundance |
| SRR38463714 | Candidozyma auris | 99.22% | 1,063,011 | 1,063,011 | 498019 | Bracken species-level abundance |
| SRR38463716 | Candidozyma auris | 99.45% | 1,330,019 | 1,330,019 | 498019 | Bracken species-level abundance |
| SRR38770855 | Candidozyma auris | 99.53% | 958,494 | 958,494 | 498019 | Bracken species-level abundance |
| SRR38770856 | Candidozyma auris | 99.41% | 1,415,431 | 1,415,431 | 498019 | Bracken species-level abundance |
| SRR38770857 | Candidozyma auris | 99.64% | 1,040,502 | 1,040,502 | 498019 | Bracken species-level abundance |
| SRR38770858 | Candidozyma auris | 99.58% | 812,516 | 812,516 | 498019 | Bracken species-level abundance |
| SRR38770859 | Candidozyma auris | 99.75% | 1,011,922 | 1,011,922 | 498019 | Bracken species-level abundance |
| SRR38770860 | Candidozyma auris | 99.00% | 758,923 | 758,923 | 498019 | Bracken species-level abundance |
| SRR38770861 | Candidozyma auris | 99.64% | 1,135,562 | 1,135,562 | 498019 | Bracken species-level abundance |
| SRR38770862 | Candidozyma auris | 99.18% | 819,552 | 819,552 | 498019 | Bracken species-level abundance |
| SRR38770863 | Candidozyma auris | 99.70% | 1,449,637 | 1,449,637 | 498019 | Bracken species-level abundance |
| SRR38770864 | Candidozyma auris | 99.34% | 881,573 | 881,573 | 498019 | Bracken species-level abundance |
6. MEGAHIT assembly summary
| Sample | contigs | Total bp | N50 | Largest contig |
|---|---|---|---|---|
| ERR263534 | 1,234 | 14,779,143 | 57,289 | 246,949 |
| ERR331060 | 427 | 11,615,434 | 67,770 | 166,550 |
| SRR25474571 | 853 | 12,899,015 | 33,626 | 165,541 |
| SRR25474602 | 951 | 12,917,299 | 28,822 | 121,549 |
| SRR25474605 | 1,070 | 12,964,591 | 24,883 | 166,191 |
| SRR38463714 | 126 | 12,344,975 | 187,990 | 793,130 |
| SRR38463716 | 130 | 12,364,545 | 254,478 | 675,766 |
| SRR38770855 | 812 | 12,515,546 | 29,270 | 113,656 |
| SRR38770856 | 737 | 12,528,879 | 30,299 | 133,475 |
| SRR38770857 | 797 | 12,545,650 | 29,892 | 105,493 |
| SRR38770858 | 819 | 12,552,458 | 29,237 | 100,950 |
| SRR38770859 | 838 | 12,550,545 | 25,695 | 100,592 |
| SRR38770860 | 820 | 12,537,710 | 28,474 | 89,904 |
| SRR38770861 | 794 | 12,549,618 | 28,263 | 126,117 |
| SRR38770862 | 840 | 12,536,638 | 27,503 | 121,623 |
| SRR38770863 | 747 | 12,554,832 | 32,589 | 155,802 |
| SRR38770864 | 852 | 12,545,301 | 27,621 | 106,446 |
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 |
|---|---|---|---|---|---|
| ERR263534 | 1,234 | 246,949 | 14,779,143 | 33.43 | 57,289 |
| ERR331060 | 427 | 166,550 | 11,615,434 | 38.08 | 67,770 |
| SRR25474571 | 853 | 165,541 | 12,899,015 | 38.63 | 33,626 |
| SRR25474602 | 951 | 121,549 | 12,917,299 | 38.61 | 28,822 |
| SRR25474605 | 1,070 | 166,191 | 12,964,591 | 38.61 | 24,883 |
| SRR38463714 | 126 | 793,130 | 12,344,975 | 45.14 | 187,990 |
| SRR38463716 | 130 | 675,766 | 12,364,545 | 45.14 | 254,478 |
| SRR38770855 | 812 | 113,656 | 12,515,546 | 44.94 | 29,270 |
| SRR38770856 | 737 | 133,475 | 12,528,879 | 44.94 | 30,299 |
| SRR38770857 | 797 | 105,493 | 12,545,650 | 44.92 | 29,892 |
| SRR38770858 | 819 | 100,950 | 12,552,458 | 44.92 | 29,237 |
| SRR38770859 | 838 | 100,592 | 12,550,545 | 44.92 | 25,695 |
| SRR38770860 | 820 | 89,904 | 12,537,710 | 44.92 | 28,474 |
| SRR38770861 | 794 | 126,117 | 12,549,618 | 44.92 | 28,263 |
| SRR38770862 | 840 | 121,623 | 12,536,638 | 44.93 | 27,503 |
| SRR38770863 | 747 | 155,802 | 12,554,832 | 44.92 | 32,589 |
| SRR38770864 | 852 | 106,446 | 12,545,301 | 44.90 | 27,621 |
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 |
|---|---|---|---|---|---|---|---|---|
| ERR263534 | 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/ERR263534.ChroQueTas/ERR263534.contigs.ChroQueTaS.Cyp51.1.tsv:437 |
| ERR331060 | Nakaseomyces glabratus | 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/ERR331060.ChroQueTas.AMR_summary.tsv No AMR mutations found in ERR331060.contigs |
| SRR25474571 | 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/SRR25474571.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR25474571.contigs |
| SRR25474602 | 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/SRR25474602.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR25474602.contigs |
| SRR25474605 | 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/SRR25474605.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR25474605.contigs |
| SRR38463714 | Candidozyma auris | azole | fluconazole/other azoles | Cyp51 | K143R | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 K143R (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(2/NA),Voriconazole(2/NA). Source: amr_out/SRR38463714.ChroQueTas/SRR38463714.contigs.ChroQueTaS.Cyp51.1.tsv:143 |
| SRR38463716 | Candidozyma auris | azole | fluconazole/other azoles | Cyp51 | V125A | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 V125A (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-2),Itraconazole(NA/-2),Posaconazole(NA/-2),Voriconazole(NA/-2). Source: amr_out/SRR38463716.ChroQueTas/SRR38463716.contigs.ChroQueTaS.Cyp51.1.tsv:125 |
| SRR38770855 | Candidozyma auris | azole/echinocandin/polyene/flucytosine | fluconazole/other azoles/echinocandins/amphotericin_B/flucytosine | Cyp51 | Y132F | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 Y132F (FungAMR MUTATION). Drug evidence from ChroQueTas: 5-fluorocytosine(NA/-8),Amphotericin_B(8/-8),Anidulafungin(NA/-8),Caspofungin(8/-8),Fluconazole(2/-8),Itraconazole(8/-8),Micafungin(NA/-8),Posaconazole(8/-8),Voriconazole(2/-8). Source: amr_out/SRR38770855.ChroQueTas/SRR38770855.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| SRR38770856 | Candidozyma auris | azole/echinocandin/polyene/flucytosine | fluconazole/other azoles/echinocandins/amphotericin_B/flucytosine | Cyp51 | Y132F | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 Y132F (FungAMR MUTATION). Drug evidence from ChroQueTas: 5-fluorocytosine(NA/-8),Amphotericin_B(8/-8),Anidulafungin(NA/-8),Caspofungin(8/-8),Fluconazole(2/-8),Itraconazole(8/-8),Micafungin(NA/-8),Posaconazole(8/-8),Voriconazole(2/-8). Source: amr_out/SRR38770856.ChroQueTas/SRR38770856.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| SRR38770857 | Candidozyma auris | azole | fluconazole/other azoles | Cyp51 | K143R | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 K143R (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(2/NA),Voriconazole(2/NA). Source: amr_out/SRR38770857.ChroQueTas/SRR38770857.contigs.ChroQueTaS.Cyp51.1.tsv:143 |
| SRR38770858 | Candidozyma auris | azole | fluconazole/other azoles | Cyp51 | V125A | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 V125A (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-2),Itraconazole(NA/-2),Posaconazole(NA/-2),Voriconazole(NA/-2). Source: amr_out/SRR38770858.ChroQueTas/SRR38770858.contigs.ChroQueTaS.Cyp51.1.tsv:125 |
| SRR38770859 | Candidozyma auris | azole/echinocandin/polyene/flucytosine | fluconazole/other azoles/echinocandins/amphotericin_B/flucytosine | Cyp51 | Y132F | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 Y132F (FungAMR MUTATION). Drug evidence from ChroQueTas: 5-fluorocytosine(NA/-8),Amphotericin_B(8/-8),Anidulafungin(NA/-8),Caspofungin(8/-8),Fluconazole(2/-8),Itraconazole(8/-8),Micafungin(NA/-8),Posaconazole(8/-8),Voriconazole(2/-8). Source: amr_out/SRR38770859.ChroQueTas/SRR38770859.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| SRR38770860 | Candidozyma auris | azole/echinocandin/polyene/flucytosine | fluconazole/other azoles/echinocandins/amphotericin_B/flucytosine | Cyp51 | Y132F | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 Y132F (FungAMR MUTATION). Drug evidence from ChroQueTas: 5-fluorocytosine(NA/-8),Amphotericin_B(8/-8),Anidulafungin(NA/-8),Caspofungin(8/-8),Fluconazole(2/-8),Itraconazole(8/-8),Micafungin(NA/-8),Posaconazole(8/-8),Voriconazole(2/-8). Source: amr_out/SRR38770860.ChroQueTas/SRR38770860.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| SRR38770861 | Candidozyma auris | azole | fluconazole/other azoles | Cyp51 | V125A | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 V125A (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-2),Itraconazole(NA/-2),Posaconazole(NA/-2),Voriconazole(NA/-2). Source: amr_out/SRR38770861.ChroQueTas/SRR38770861.contigs.ChroQueTaS.Cyp51.1.tsv:125 |
| SRR38770862 | Candidozyma auris | azole/echinocandin/polyene/flucytosine | fluconazole/other azoles/echinocandins/amphotericin_B/flucytosine | Cyp51 | Y132F | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 Y132F (FungAMR MUTATION). Drug evidence from ChroQueTas: 5-fluorocytosine(NA/-8),Amphotericin_B(8/-8),Anidulafungin(NA/-8),Caspofungin(8/-8),Fluconazole(2/-8),Itraconazole(8/-8),Micafungin(NA/-8),Posaconazole(8/-8),Voriconazole(2/-8). Source: amr_out/SRR38770862.ChroQueTas/SRR38770862.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| SRR38770863 | Candidozyma auris | azole | fluconazole/other azoles | Cyp51 | V125A | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 V125A (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-2),Itraconazole(NA/-2),Posaconazole(NA/-2),Voriconazole(NA/-2). Source: amr_out/SRR38770863.ChroQueTas/SRR38770863.contigs.ChroQueTaS.Cyp51.1.tsv:125 |
| SRR38770864 | Candidozyma auris | azole/echinocandin/polyene/flucytosine | fluconazole/other azoles/echinocandins/amphotericin_B/flucytosine | Cyp51 | Y132F | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 Y132F (FungAMR MUTATION). Drug evidence from ChroQueTas: 5-fluorocytosine(NA/-8),Amphotericin_B(8/-8),Anidulafungin(NA/-8),Caspofungin(8/-8),Fluconazole(2/-8),Itraconazole(8/-8),Micafungin(NA/-8),Posaconazole(8/-8),Voriconazole(2/-8). Source: amr_out/SRR38770864.ChroQueTas/SRR38770864.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
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 | 3 | 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 | SKIPPED_TOO_FEW_SAMPLES | 1 | snippy_core | 1 | NA | Requires at least 3 samples for a species-specific tree. |
| Candidozyma auris | PASS | 12 | snippy_core_rc170_tb_style | NA | 78438 | 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. |
| Nakaseomyces glabratus | SKIPPED_TOO_FEW_SAMPLES | 1 | haploid_bcftools_consensus | 1 | NA | Requires at least 3 samples for a species-specific tree. |
Candidozyma auris
Species without a displayed tree:
- Candida parapsilosis: SKIPPED_SPECIES_NOT_IN_REFERENCE_MANIFEST; samples after species-specific consensus/eligibility = 3; 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 albicans: 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.
- Nakaseomyces glabratus: SKIPPED_TOO_FEW_SAMPLES; samples after species-specific consensus/eligibility = 1; branch = haploid_bcftools_consensus; 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 |
|---|---|---|---|---|
| Candidozyma auris | SRR38463714 | SRR38770857 | 262 | Distinct / review with metadata |
| Candidozyma auris | SRR38463716 | SRR38770863 | 103 | Distinct / review with metadata |
| Candidozyma auris | SRR38770855 | SRR38770856 | 110 | Distinct / review with metadata |
| Candidozyma auris | SRR38770856 | SRR38770864 | 96 | Distinct / review with metadata |
| Candidozyma auris | SRR38770857 | SRR38770856 | 223 | Distinct / review with metadata |
| Candidozyma auris | SRR38770858 | SRR38770863 | 48 | Distinct / review with metadata |
| Candidozyma auris | SRR38770859 | SRR38770862 | 80 | Distinct / review with metadata |
| Candidozyma auris | SRR38770860 | SRR38770859 | 109 | Distinct / review with metadata |
| Candidozyma auris | SRR38770861 | SRR38770863 | 49 | Distinct / review with metadata |
| Candidozyma auris | SRR38770862 | SRR38770859 | 80 | Distinct / review with metadata |
| Candidozyma auris | SRR38770863 | SRR38770858 | 48 | Distinct / review with metadata |
| Candidozyma auris | SRR38770864 | SRR38770856 | 96 | Distinct / review with metadata |
Pairwise SNP-distance matrix/table
| species | Sample A | Sample B | SNP distance | Compared core-SNP sites |
|---|---|---|---|---|
| Candidozyma auris | SRR38463714 | SRR38463716 | 39809 | 78438 |
| Candidozyma auris | SRR38463714 | SRR38770855 | 355 | 78438 |
| Candidozyma auris | SRR38463714 | SRR38770856 | 355 | 78438 |
| Candidozyma auris | SRR38463714 | SRR38770857 | 262 | 78438 |
| Candidozyma auris | SRR38463714 | SRR38770858 | 39791 | 78438 |
| Candidozyma auris | SRR38463714 | SRR38770859 | 329 | 78438 |
| Candidozyma auris | SRR38463714 | SRR38770860 | 388 | 78438 |
| Candidozyma auris | SRR38463714 | SRR38770861 | 39804 | 78438 |
| Candidozyma auris | SRR38463714 | SRR38770862 | 377 | 78438 |
| Candidozyma auris | SRR38463714 | SRR38770863 | 39797 | 78438 |
| Candidozyma auris | SRR38463714 | SRR38770864 | 361 | 78438 |
| Candidozyma auris | SRR38463716 | SRR38770855 | 39814 | 78438 |
| Candidozyma auris | SRR38463716 | SRR38770856 | 39829 | 78438 |
| Candidozyma auris | SRR38463716 | SRR38770857 | 39795 | 78438 |
| Candidozyma auris | SRR38463716 | SRR38770858 | 107 | 78438 |
| Candidozyma auris | SRR38463716 | SRR38770859 | 39779 | 78438 |
| Candidozyma auris | SRR38463716 | SRR38770860 | 39822 | 78438 |
| Candidozyma auris | SRR38463716 | SRR38770861 | 106 | 78438 |
| Candidozyma auris | SRR38463716 | SRR38770862 | 39803 | 78438 |
| Candidozyma auris | SRR38463716 | SRR38770863 | 103 | 78438 |
| Candidozyma auris | SRR38463716 | SRR38770864 | 39818 | 78438 |
| Candidozyma auris | SRR38770855 | SRR38770856 | 110 | 78438 |
| Candidozyma auris | SRR38770855 | SRR38770857 | 227 | 78438 |
| Candidozyma auris | SRR38770855 | SRR38770858 | 39790 | 78438 |
| Candidozyma auris | SRR38770855 | SRR38770859 | 116 | 78438 |
| Candidozyma auris | SRR38770855 | SRR38770860 | 135 | 78438 |
| Candidozyma auris | SRR38770855 | SRR38770861 | 39791 | 78438 |
| Candidozyma auris | SRR38770855 | SRR38770862 | 128 | 78438 |
| Candidozyma auris | SRR38770855 | SRR38770863 | 39796 | 78438 |
| Candidozyma auris | SRR38770855 | SRR38770864 | 116 | 78438 |
| Candidozyma auris | SRR38770856 | SRR38770857 | 223 | 78438 |
| Candidozyma auris | SRR38770856 | SRR38770858 | 39801 | 78438 |
| Candidozyma auris | SRR38770856 | SRR38770859 | 114 | 78438 |
| Candidozyma auris | SRR38770856 | SRR38770860 | 124 | 78438 |
| Candidozyma auris | SRR38770856 | SRR38770861 | 39810 | 78438 |
| Candidozyma auris | SRR38770856 | SRR38770862 | 132 | 78438 |
| Candidozyma auris | SRR38770856 | SRR38770863 | 39811 | 78438 |
| Candidozyma auris | SRR38770856 | SRR38770864 | 96 | 78438 |
| Candidozyma auris | SRR38770857 | SRR38770858 | 39767 | 78438 |
| Candidozyma auris | SRR38770857 | SRR38770859 | 227 | 78438 |
| Candidozyma auris | SRR38770857 | SRR38770860 | 260 | 78438 |
| Candidozyma auris | SRR38770857 | SRR38770861 | 39784 | 78438 |
| Candidozyma auris | SRR38770857 | SRR38770862 | 245 | 78438 |
| Candidozyma auris | SRR38770857 | SRR38770863 | 39777 | 78438 |
| Candidozyma auris | SRR38770857 | SRR38770864 | 233 | 78438 |
| Candidozyma auris | SRR38770858 | SRR38770859 | 39751 | 78438 |
| Candidozyma auris | SRR38770858 | SRR38770860 | 39798 | 78438 |
| Candidozyma auris | SRR38770858 | SRR38770861 | 53 | 78438 |
| Candidozyma auris | SRR38770858 | SRR38770862 | 39775 | 78438 |
| Candidozyma auris | SRR38770858 | SRR38770863 | 48 | 78438 |
| Candidozyma auris | SRR38770858 | SRR38770864 | 39794 | 78438 |
| Candidozyma auris | SRR38770859 | SRR38770860 | 109 | 78438 |
| Candidozyma auris | SRR38770859 | SRR38770861 | 39768 | 78438 |
| Candidozyma auris | SRR38770859 | SRR38770862 | 80 | 78438 |
| Candidozyma auris | SRR38770859 | SRR38770863 | 39761 | 78438 |
| Candidozyma auris | SRR38770859 | SRR38770864 | 110 | 78438 |
| Candidozyma auris | SRR38770860 | SRR38770861 | 39811 | 78438 |
| Candidozyma auris | SRR38770860 | SRR38770862 | 129 | 78438 |
| Candidozyma auris | SRR38770860 | SRR38770863 | 39804 | 78438 |
| Candidozyma auris | SRR38770860 | SRR38770864 | 118 | 78438 |
| Candidozyma auris | SRR38770861 | SRR38770862 | 39792 | 78438 |
| Candidozyma auris | SRR38770861 | SRR38770863 | 49 | 78438 |
| Candidozyma auris | SRR38770861 | SRR38770864 | 39807 | 78438 |
| Candidozyma auris | SRR38770862 | SRR38770863 | 39785 | 78438 |
| Candidozyma auris | SRR38770862 | SRR38770864 | 114 | 78438 |
| Candidozyma auris | SRR38770863 | SRR38770864 | 39800 | 78438 |
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.