Samples analyzed25
Top species groups7
Total AMR hits14
Median N5034,720
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 auris13
Nakaseomyces glabratus4
Candida albicans2
Candida tropicalis2
Clavispora lusitaniae2
Pichia kudriavzevii1
Candida parapsilosis1
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 |
|---|---|---|---|---|---|---|---|---|---|---|
| ERR2300788 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| ERR2300806 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| ERR2300807 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| ERR2300808 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| ERR2300809 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| ERR2300810 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| ERR2300812 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| ERR2300813 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| ERR2300814 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| ERR263535 | NA | NA | Candida albicans | High | Review | Review | 1 marker(s) | Excluded | Review | QUAST assembly QC; AMR marker detected |
| ERR3040852 | NA | NA | Pichia kudriavzevii | Low / review | Review | Review | No curated marker detected | Excluded | Review | species confidence; QUAST assembly QC |
| ERR331060 | NA | NA | Nakaseomyces glabratus | Low / review | Pass | Pass | No curated marker detected | Review | Review | species confidence |
| ERR331061 | NA | NA | Nakaseomyces glabratus | Low / review | Pass | Pass | No curated marker detected | Review | Review | species confidence |
| ERR570065 | NA | NA | Nakaseomyces glabratus | Low / review | Pass | Pass | No curated marker detected | Review | Review | species confidence |
| SRR10967506 | NA | NA | Candida tropicalis | 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 |
| SRR10967518 | NA | NA | Candida tropicalis | 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 |
| SRR11092001 | NA | NA | Candidozyma auris | Low / review | Pass | Pass | No curated marker detected | Included / eligible | Review | species confidence |
| SRR11235423 | NA | NA | Nakaseomyces glabratus | High | Pass | Pass | 1 marker(s) | Review | Review | AMR marker detected |
| SRR11235431 | NA | NA | Candida albicans | High | Review | Review | 1 marker(s) | Excluded | Review | QUAST assembly QC; AMR marker detected |
| SRR25474587 | NA | NA | Candida parapsilosis | High | Review | Review | No curated marker detected | Excluded | Review | QUAST assembly QC |
| SRR38908326 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38908330 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38908334 | NA | NA | Candidozyma auris | High | Pass | Pass | No curated marker detected | Included / eligible | Ready for surveillance interpretation | No major automated warning flags using species typing, QUAST assembly QC, AMR screening, and phylogeny status |
| SRR6475853 | NA | NA | Clavispora lusitaniae | Low / review | Pass | Pass | No curated marker detected | Excluded | Review | species confidence |
| SRR6476030 | NA | NA | Clavispora lusitaniae | Low / review | Pass | Pass | No curated marker detected | Excluded | Review | species confidence |
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
ERR2300788
Candidozyma auris Review
Species reads99.52%
Contigs670
N5033,153
GC (%)44.95
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 (13 samples)
ERR2300806
Candidozyma auris Review
Species reads98.61%
Contigs688
N5032,749
GC (%)44.95
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 (13 samples)
ERR2300807
Candidozyma auris Review
Species reads98.97%
Contigs659
N5034,720
GC (%)44.95
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 (13 samples)
ERR2300808
Candidozyma auris Review
Species reads98.32%
Contigs677
N5033,038
GC (%)44.95
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 (13 samples)
ERR2300809
Candidozyma auris Review
Species reads98.72%
Contigs695
N5031,632
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 (13 samples)
ERR2300810
Candidozyma auris Review
Species reads99.14%
Contigs688
N5030,447
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 (13 samples)
ERR2300812
Candidozyma auris Review
Species reads99.57%
Contigs653
N5032,986
GC (%)44.95
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 (13 samples)
ERR2300813
Candidozyma auris Review
Species reads99.45%
Contigs687
N5031,998
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 (13 samples)
ERR2300814
Candidozyma auris Review
Species reads99.49%
Contigs655
N5033,916
GC (%)44.96
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 (13 samples)
ERR263535
Candida albicans Review
Species reads99.44%
Contigs2,777
N5013,483
GC (%)33.86
1 AMR hit(s) Species confidence: High Phylogeny: Excluded
Interpretation: QUAST assembly QC; AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Requires at least 3 samples for a species-specific tree.
ERR3040852
Pichia kudriavzevii Review
Species reads34.89%
Contigs5,146
N5054,792
GC (%)49.64
No curated genomic AMR marker detected — not susceptible Species confidence: Low / review Phylogeny: Excluded
Interpretation: species confidence; QUAST assembly QC. 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.
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: Review
Interpretation: species confidence. Species note: Top species abundance <80%; possible mixed sample, contamination, or weak species assignment. Phylogeny note: Consensus FASTA lengths differ after reference-based consensus generation.
ERR331061
Nakaseomyces glabratus Review
Species reads73.69%
Contigs433
N5071,482
GC (%)38.08
No curated genomic AMR marker detected — not susceptible Species confidence: Low / review Phylogeny: Review
Interpretation: species confidence. Species note: Top species abundance <80%; possible mixed sample, contamination, or weak species assignment. Phylogeny note: Consensus FASTA lengths differ after reference-based consensus generation.
ERR570065
Nakaseomyces glabratus Review
Species reads73.63%
Contigs430
N5068,055
GC (%)38.08
No curated genomic AMR marker detected — not susceptible Species confidence: Low / review Phylogeny: Review
Interpretation: species confidence. Species note: Top species abundance <80%; possible mixed sample, contamination, or weak species assignment. Phylogeny note: Consensus FASTA lengths differ after reference-based consensus generation.
SRR10967506
Candida tropicalis Ready for surveillance interpretation
Species reads99.86%
Contigs872
N5059,289
GC (%)33.04
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: Requires at least 3 samples for a species-specific tree.
SRR10967518
Candida tropicalis Ready for surveillance interpretation
Species reads99.93%
Contigs815
N5066,770
GC (%)33.03
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: Requires at least 3 samples for a species-specific tree.
SRR11092001
Candidozyma auris Review
Species reads60.97%
Contigs322
N50118,827
GC (%)47.08
No curated genomic AMR marker detected — not susceptible Species confidence: Low / review Phylogeny: Included / eligible
Interpretation: species confidence. Species note: Top species abundance <80%; possible mixed sample, contamination, or weak species assignment. Phylogeny note: Species group passed phylogeny stage (13 samples)
SRR11235423
Nakaseomyces glabratus Review
Species reads99.99%
Contigs1,264
N5031,653
GC (%)38.83
1 AMR hit(s) Species confidence: High Phylogeny: Review
Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Consensus FASTA lengths differ after reference-based consensus generation.
SRR11235431
Candida albicans Review
Species reads99.30%
Contigs4,091
N5012,510
GC (%)33.85
1 AMR hit(s) Species confidence: High Phylogeny: Excluded
Interpretation: QUAST assembly QC; AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Requires at least 3 samples for a species-specific tree.
SRR25474587
Candida parapsilosis Review
Species reads100.00%
Contigs1,392
N5019,980
GC (%)38.61
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: 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.
SRR38908326
Candidozyma auris Review
Species reads99.37%
Contigs115
N50209,202
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 (13 samples)
SRR38908330
Candidozyma auris Review
Species reads99.25%
Contigs117
N50270,319
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 (13 samples)
SRR38908334
Candidozyma auris Ready for surveillance interpretation
Species reads99.16%
Contigs146
N50144,269
GC (%)45.15
No curated genomic AMR marker detected — not susceptible Species confidence: High Phylogeny: Included / eligible
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: Species group passed phylogeny stage (13 samples)
SRR6475853
Clavispora lusitaniae Review
Species reads55.62%
Contigs54
N50609,454
GC (%)45.52
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.
SRR6476030
Clavispora lusitaniae Review
Species reads54.11%
Contigs161
N50240,220
GC (%)46.15
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.
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 |
|---|---|---|---|---|---|---|
| ERR2300788 | Candidozyma auris | 99.52% | 5,062,165 | 5,062,165 | 498019 | Bracken species-level abundance |
| ERR2300806 | Candidozyma auris | 98.61% | 5,042,095 | 5,042,095 | 498019 | Bracken species-level abundance |
| ERR2300807 | Candidozyma auris | 98.97% | 5,231,079 | 5,231,079 | 498019 | Bracken species-level abundance |
| ERR2300808 | Candidozyma auris | 98.32% | 5,035,032 | 5,035,032 | 498019 | Bracken species-level abundance |
| ERR2300809 | Candidozyma auris | 98.72% | 6,247,874 | 6,247,874 | 498019 | Bracken species-level abundance |
| ERR2300810 | Candidozyma auris | 99.14% | 6,041,370 | 6,041,370 | 498019 | Bracken species-level abundance |
| ERR2300812 | Candidozyma auris | 99.57% | 5,103,087 | 5,103,087 | 498019 | Bracken species-level abundance |
| ERR2300813 | Candidozyma auris | 99.45% | 4,994,307 | 4,994,307 | 498019 | Bracken species-level abundance |
| ERR2300814 | Candidozyma auris | 99.49% | 5,038,951 | 5,038,951 | 498019 | Bracken species-level abundance |
| ERR263535 | Candida albicans | 99.44% | 1,749,331 | 1,749,331 | 5476 | Bracken species-level abundance |
| ERR3040852 | Pichia kudriavzevii | 34.89% | 6,669 | 6,669 | 4909 | Bracken species-level abundance |
| ERR331060 | Nakaseomyces glabratus | 73.73% | 190,301 | 190,301 | 5478 | Bracken species-level abundance |
| ERR331061 | Nakaseomyces glabratus | 73.69% | 178,423 | 178,423 | 5478 | Bracken species-level abundance |
| ERR570065 | Nakaseomyces glabratus | 73.63% | 154,728 | 154,728 | 5478 | Bracken species-level abundance |
| SRR10967506 | Candida tropicalis | 99.86% | 2,260,451 | 2,260,451 | 5482 | Bracken species-level abundance |
| SRR10967518 | Candida tropicalis | 99.93% | 2,129,099 | 2,129,099 | 5482 | Bracken species-level abundance |
| SRR11092001 | Candidozyma auris | 60.97% | 42,729 | 42,729 | 498019 | Bracken species-level abundance |
| SRR11235423 | Nakaseomyces glabratus | 99.99% | 1,676,791 | 1,676,791 | 5478 | Bracken species-level abundance |
| SRR11235431 | Candida albicans | 99.30% | 2,986,292 | 2,986,292 | 5476 | Bracken species-level abundance |
| SRR25474587 | Candida parapsilosis | 100.00% | 1,217,556 | 1,217,556 | 5480 | Bracken species-level abundance |
| SRR38908326 | Candidozyma auris | 99.37% | 1,244,445 | 1,244,445 | 498019 | Bracken species-level abundance |
| SRR38908330 | Candidozyma auris | 99.25% | 1,287,429 | 1,287,429 | 498019 | Bracken species-level abundance |
| SRR38908334 | Candidozyma auris | 99.16% | 1,052,473 | 1,052,473 | 498019 | Bracken species-level abundance |
| SRR6475853 | Clavispora lusitaniae | 55.62% | 19,642 | 19,642 | 36911 | Bracken species-level abundance |
| SRR6476030 | Clavispora lusitaniae | 54.11% | 45,001 | 45,001 | 36911 | Bracken species-level abundance |
6. MEGAHIT assembly summary
| Sample | contigs | Total bp | N50 | Largest contig |
|---|---|---|---|---|
| ERR2300788 | 670 | 12,407,992 | 33,153 | 126,993 |
| ERR2300806 | 688 | 12,394,995 | 32,749 | 140,237 |
| ERR2300807 | 659 | 12,407,021 | 34,720 | 127,023 |
| ERR2300808 | 677 | 12,409,566 | 33,038 | 142,154 |
| ERR2300809 | 695 | 12,419,101 | 31,632 | 106,491 |
| ERR2300810 | 688 | 12,414,152 | 30,447 | 174,120 |
| ERR2300812 | 653 | 12,407,002 | 32,986 | 115,417 |
| ERR2300813 | 687 | 12,410,993 | 31,998 | 133,252 |
| ERR2300814 | 655 | 12,403,236 | 33,916 | 129,535 |
| ERR263535 | 2,777 | 13,941,321 | 13,483 | 132,505 |
| ERR3040852 | 5,146 | 13,603,315 | 54,792 | 367,079 |
| ERR331060 | 427 | 11,615,434 | 67,770 | 166,550 |
| ERR331061 | 433 | 11,618,740 | 71,482 | 269,717 |
| ERR570065 | 430 | 11,617,895 | 68,055 | 229,603 |
| SRR10967506 | 872 | 14,597,396 | 59,289 | 262,902 |
| SRR10967518 | 815 | 14,557,604 | 66,770 | 251,077 |
| SRR11092001 | 322 | 12,796,469 | 118,827 | 423,624 |
| SRR11235423 | 1,264 | 12,445,096 | 31,653 | 116,487 |
| SRR11235431 | 4,091 | 15,459,067 | 12,510 | 88,610 |
| SRR25474587 | 1,392 | 13,028,120 | 19,980 | 105,575 |
| SRR38908326 | 115 | 12,333,174 | 209,202 | 876,588 |
| SRR38908330 | 117 | 12,343,577 | 270,319 | 781,411 |
| SRR38908334 | 146 | 12,262,768 | 144,269 | 441,195 |
| SRR6475853 | 54 | 9,654,719 | 609,454 | 1,021,854 |
| SRR6476030 | 161 | 11,704,652 | 240,220 | 598,301 |
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 |
|---|---|---|---|---|---|
| ERR2300788 | 670 | 126,993 | 12,407,992 | 44.95 | 33,153 |
| ERR2300806 | 688 | 140,237 | 12,394,995 | 44.95 | 32,749 |
| ERR2300807 | 659 | 127,023 | 12,407,021 | 44.95 | 34,720 |
| ERR2300808 | 677 | 142,154 | 12,409,566 | 44.95 | 33,038 |
| ERR2300809 | 695 | 106,491 | 12,419,101 | 44.93 | 31,632 |
| ERR2300810 | 688 | 174,120 | 12,414,152 | 44.93 | 30,447 |
| ERR2300812 | 653 | 115,417 | 12,407,002 | 44.95 | 32,986 |
| ERR2300813 | 687 | 133,252 | 12,410,993 | 44.94 | 31,998 |
| ERR2300814 | 655 | 129,535 | 12,403,236 | 44.96 | 33,916 |
| ERR263535 | 2,777 | 132,505 | 13,941,321 | 33.86 | 13,483 |
| ERR3040852 | 5,146 | 367,079 | 13,603,315 | 49.64 | 54,792 |
| ERR331060 | 427 | 166,550 | 11,615,434 | 38.08 | 67,770 |
| ERR331061 | 433 | 269,717 | 11,618,740 | 38.08 | 71,482 |
| ERR570065 | 430 | 229,603 | 11,617,895 | 38.08 | 68,055 |
| SRR10967506 | 872 | 262,902 | 14,597,396 | 33.04 | 59,289 |
| SRR10967518 | 815 | 251,077 | 14,557,604 | 33.03 | 66,770 |
| SRR11092001 | 322 | 423,624 | 12,796,469 | 47.08 | 118,827 |
| SRR11235423 | 1,264 | 116,487 | 12,445,096 | 38.83 | 31,653 |
| SRR11235431 | 4,091 | 88,610 | 15,459,067 | 33.85 | 12,510 |
| SRR25474587 | 1,392 | 105,575 | 13,028,120 | 38.61 | 19,980 |
| SRR38908326 | 115 | 876,588 | 12,333,174 | 45.14 | 209,202 |
| SRR38908330 | 117 | 781,411 | 12,343,577 | 45.14 | 270,319 |
| SRR38908334 | 146 | 441,195 | 12,262,768 | 45.15 | 144,269 |
| SRR6475853 | 54 | 1,021,854 | 9,654,719 | 45.52 | 609,454 |
| SRR6476030 | 161 | 598,301 | 11,704,652 | 46.15 | 240,220 |
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 |
|---|---|---|---|---|---|---|---|---|
| ERR2300788 | 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/ERR2300788.ChroQueTas/ERR2300788.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| ERR2300806 | 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/ERR2300806.ChroQueTas/ERR2300806.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| ERR2300807 | 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/ERR2300807.ChroQueTas/ERR2300807.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| ERR2300808 | 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/ERR2300808.ChroQueTas/ERR2300808.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| ERR2300809 | 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/ERR2300809.ChroQueTas/ERR2300809.contigs.ChroQueTaS.Cyp51.1.tsv:125 |
| ERR2300810 | 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/ERR2300810.ChroQueTas/ERR2300810.contigs.ChroQueTaS.Cyp51.1.tsv:125 |
| ERR2300812 | 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/ERR2300812.ChroQueTas/ERR2300812.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| ERR2300813 | 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/ERR2300813.ChroQueTas/ERR2300813.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| ERR2300814 | 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/ERR2300814.ChroQueTas/ERR2300814.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| ERR263535 | 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/ERR263535.ChroQueTas/ERR263535.contigs.ChroQueTaS.Cyp51.1.tsv:266 |
| ERR3040852 | Pichia kudriavzevii | 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/ERR3040852.ChroQueTas.AMR_summary.tsv No AMR mutations found in ERR3040852.contigs |
| 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 |
| ERR331061 | 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/ERR331061.ChroQueTas.AMR_summary.tsv No AMR mutations found in ERR331061.contigs |
| ERR570065 | 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/ERR570065.ChroQueTas.AMR_summary.tsv No AMR mutations found in ERR570065.contigs |
| SRR10967506 | 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/SRR10967506.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR10967506.contigs |
| SRR10967518 | 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/SRR10967518.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR10967518.contigs |
| SRR11092001 | Candidozyma auris | 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/SRR11092001.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR11092001.contigs |
| SRR11235423 | Nakaseomyces glabratus | antifungal | species-aware antifungal panel | Ben1 | V254I | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Ben1 V254I (FungAMR MUTATION). Drug evidence from ChroQueTas: Various(NA/-8). Source: amr_out/SRR11235423.ChroQueTas/SRR11235423.contigs.ChroQueTaS.Ben1.1.tsv:254 |
| SRR11235431 | 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/SRR11235431.ChroQueTas/SRR11235431.contigs.ChroQueTaS.Cyp51.1.tsv:266 |
| SRR25474587 | 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/SRR25474587.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR25474587.contigs |
| SRR38908326 | 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/SRR38908326.ChroQueTas/SRR38908326.contigs.ChroQueTaS.Cyp51.1.tsv:125 |
| SRR38908330 | 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/SRR38908330.ChroQueTas/SRR38908330.contigs.ChroQueTaS.Cyp51.1.tsv:143 |
| SRR38908334 | Candidozyma auris | 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/SRR38908334.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR38908334.contigs |
| SRR6475853 | Clavispora lusitaniae | 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/SRR6475853.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR6475853.contigs |
| SRR6476030 | Clavispora lusitaniae | 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/SRR6476030.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR6476030.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 | SKIPPED_TOO_FEW_SAMPLES | 2 | snippy_core | 1 | NA | Requires at least 3 samples for a species-specific tree. |
| Candida tropicalis | SKIPPED_TOO_FEW_SAMPLES | 2 | snippy_core | 1 | NA | Requires at least 3 samples for a species-specific tree. |
| Candidozyma auris | PASS | 13 | snippy_core_rc170_tb_style | NA | 27811 | 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. |
| Clavispora lusitaniae | SKIPPED_TOO_FEW_SAMPLES | 2 | diploid_aware_bcftools_iupac_consensus | 2 | NA | Requires at least 3 samples for a species-specific tree. |
| Nakaseomyces glabratus | FAILED_CORE_SNP_ALIGNMENT | 4 | haploid_bcftools_consensus | 1 | NA | Consensus FASTA lengths differ after reference-based consensus generation. |
| Pichia kudriavzevii | SKIPPED_TOO_FEW_SAMPLES | 1 | diploid_aware_bcftools_iupac_consensus | 2 | 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 = 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 albicans: SKIPPED_TOO_FEW_SAMPLES; samples after species-specific consensus/eligibility = 2; branch = snippy_core; note = Requires at least 3 samples for a species-specific tree.
- Candida tropicalis: SKIPPED_TOO_FEW_SAMPLES; samples after species-specific consensus/eligibility = 2; branch = snippy_core; note = Requires at least 3 samples for a species-specific tree.
- Clavispora lusitaniae: SKIPPED_TOO_FEW_SAMPLES; samples after species-specific consensus/eligibility = 2; branch = diploid_aware_bcftools_iupac_consensus; note = Requires at least 3 samples for a species-specific tree.
- Nakaseomyces glabratus: FAILED_CORE_SNP_ALIGNMENT; samples after species-specific consensus/eligibility = 4; branch = haploid_bcftools_consensus; note = Consensus FASTA lengths differ after reference-based consensus generation.
- Pichia kudriavzevii: SKIPPED_TOO_FEW_SAMPLES; samples after species-specific consensus/eligibility = 1; branch = diploid_aware_bcftools_iupac_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 | ERR2300788 | ERR2300806 | 0 | Possible close genetic relationship |
| Candidozyma auris | ERR2300806 | ERR2300788 | 0 | Possible close genetic relationship |
| Candidozyma auris | ERR2300807 | ERR2300788 | 0 | Possible close genetic relationship |
| Candidozyma auris | ERR2300808 | ERR2300788 | 0 | Possible close genetic relationship |
| Candidozyma auris | ERR2300809 | ERR2300810 | 0 | Possible close genetic relationship |
| Candidozyma auris | ERR2300810 | ERR2300809 | 0 | Possible close genetic relationship |
| Candidozyma auris | ERR2300812 | ERR2300788 | 0 | Possible close genetic relationship |
| Candidozyma auris | ERR2300813 | ERR2300788 | 0 | Possible close genetic relationship |
| Candidozyma auris | ERR2300814 | ERR2300788 | 0 | Possible close genetic relationship |
| Candidozyma auris | SRR11092001 | ERR2300788 | 26797 | Distinct / review with metadata |
| Candidozyma auris | SRR38908326 | ERR2300809 | 2 | Possible close genetic relationship |
| Candidozyma auris | SRR38908330 | ERR2300788 | 0 | Possible close genetic relationship |
| Candidozyma auris | SRR38908334 | ERR2300788 | 1565 | Distinct / review with metadata |
Pairwise SNP-distance matrix/table
| species | Sample A | Sample B | SNP distance | Compared core-SNP sites |
|---|---|---|---|---|
| Candidozyma auris | ERR2300788 | ERR2300806 | 0 | 27811 |
| Candidozyma auris | ERR2300788 | ERR2300807 | 0 | 27811 |
| Candidozyma auris | ERR2300788 | ERR2300808 | 0 | 27811 |
| Candidozyma auris | ERR2300788 | ERR2300809 | 380 | 27811 |
| Candidozyma auris | ERR2300788 | ERR2300810 | 380 | 27811 |
| Candidozyma auris | ERR2300788 | ERR2300812 | 0 | 27811 |
| Candidozyma auris | ERR2300788 | ERR2300813 | 0 | 27811 |
| Candidozyma auris | ERR2300788 | ERR2300814 | 0 | 27811 |
| Candidozyma auris | ERR2300788 | SRR11092001 | 26797 | 27811 |
| Candidozyma auris | ERR2300788 | SRR38908326 | 382 | 27811 |
| Candidozyma auris | ERR2300788 | SRR38908330 | 0 | 27811 |
| Candidozyma auris | ERR2300788 | SRR38908334 | 1565 | 27811 |
| Candidozyma auris | ERR2300806 | ERR2300807 | 0 | 27811 |
| Candidozyma auris | ERR2300806 | ERR2300808 | 0 | 27811 |
| Candidozyma auris | ERR2300806 | ERR2300809 | 380 | 27811 |
| Candidozyma auris | ERR2300806 | ERR2300810 | 380 | 27811 |
| Candidozyma auris | ERR2300806 | ERR2300812 | 0 | 27811 |
| Candidozyma auris | ERR2300806 | ERR2300813 | 0 | 27811 |
| Candidozyma auris | ERR2300806 | ERR2300814 | 0 | 27811 |
| Candidozyma auris | ERR2300806 | SRR11092001 | 26797 | 27811 |
| Candidozyma auris | ERR2300806 | SRR38908326 | 382 | 27811 |
| Candidozyma auris | ERR2300806 | SRR38908330 | 0 | 27811 |
| Candidozyma auris | ERR2300806 | SRR38908334 | 1565 | 27811 |
| Candidozyma auris | ERR2300807 | ERR2300808 | 0 | 27811 |
| Candidozyma auris | ERR2300807 | ERR2300809 | 380 | 27811 |
| Candidozyma auris | ERR2300807 | ERR2300810 | 380 | 27811 |
| Candidozyma auris | ERR2300807 | ERR2300812 | 0 | 27811 |
| Candidozyma auris | ERR2300807 | ERR2300813 | 0 | 27811 |
| Candidozyma auris | ERR2300807 | ERR2300814 | 0 | 27811 |
| Candidozyma auris | ERR2300807 | SRR11092001 | 26797 | 27811 |
| Candidozyma auris | ERR2300807 | SRR38908326 | 382 | 27811 |
| Candidozyma auris | ERR2300807 | SRR38908330 | 0 | 27811 |
| Candidozyma auris | ERR2300807 | SRR38908334 | 1565 | 27811 |
| Candidozyma auris | ERR2300808 | ERR2300809 | 380 | 27811 |
| Candidozyma auris | ERR2300808 | ERR2300810 | 380 | 27811 |
| Candidozyma auris | ERR2300808 | ERR2300812 | 0 | 27811 |
| Candidozyma auris | ERR2300808 | ERR2300813 | 0 | 27811 |
| Candidozyma auris | ERR2300808 | ERR2300814 | 0 | 27811 |
| Candidozyma auris | ERR2300808 | SRR11092001 | 26797 | 27811 |
| Candidozyma auris | ERR2300808 | SRR38908326 | 382 | 27811 |
| Candidozyma auris | ERR2300808 | SRR38908330 | 0 | 27811 |
| Candidozyma auris | ERR2300808 | SRR38908334 | 1565 | 27811 |
| Candidozyma auris | ERR2300809 | ERR2300810 | 0 | 27811 |
| Candidozyma auris | ERR2300809 | ERR2300812 | 380 | 27811 |
| Candidozyma auris | ERR2300809 | ERR2300813 | 380 | 27811 |
| Candidozyma auris | ERR2300809 | ERR2300814 | 380 | 27811 |
| Candidozyma auris | ERR2300809 | SRR11092001 | 26832 | 27811 |
| Candidozyma auris | ERR2300809 | SRR38908326 | 2 | 27811 |
| Candidozyma auris | ERR2300809 | SRR38908330 | 380 | 27811 |
| Candidozyma auris | ERR2300809 | SRR38908334 | 1588 | 27811 |
| Candidozyma auris | ERR2300810 | ERR2300812 | 380 | 27811 |
| Candidozyma auris | ERR2300810 | ERR2300813 | 380 | 27811 |
| Candidozyma auris | ERR2300810 | ERR2300814 | 380 | 27811 |
| Candidozyma auris | ERR2300810 | SRR11092001 | 26832 | 27811 |
| Candidozyma auris | ERR2300810 | SRR38908326 | 2 | 27811 |
| Candidozyma auris | ERR2300810 | SRR38908330 | 380 | 27811 |
| Candidozyma auris | ERR2300810 | SRR38908334 | 1588 | 27811 |
| Candidozyma auris | ERR2300812 | ERR2300813 | 0 | 27811 |
| Candidozyma auris | ERR2300812 | ERR2300814 | 0 | 27811 |
| Candidozyma auris | ERR2300812 | SRR11092001 | 26797 | 27811 |
| Candidozyma auris | ERR2300812 | SRR38908326 | 382 | 27811 |
| Candidozyma auris | ERR2300812 | SRR38908330 | 0 | 27811 |
| Candidozyma auris | ERR2300812 | SRR38908334 | 1565 | 27811 |
| Candidozyma auris | ERR2300813 | ERR2300814 | 0 | 27811 |
| Candidozyma auris | ERR2300813 | SRR11092001 | 26797 | 27811 |
| Candidozyma auris | ERR2300813 | SRR38908326 | 382 | 27811 |
| Candidozyma auris | ERR2300813 | SRR38908330 | 0 | 27811 |
| Candidozyma auris | ERR2300813 | SRR38908334 | 1565 | 27811 |
| Candidozyma auris | ERR2300814 | SRR11092001 | 26797 | 27811 |
| Candidozyma auris | ERR2300814 | SRR38908326 | 382 | 27811 |
| Candidozyma auris | ERR2300814 | SRR38908330 | 0 | 27811 |
| Candidozyma auris | ERR2300814 | SRR38908334 | 1565 | 27811 |
| Candidozyma auris | SRR11092001 | SRR38908326 | 26832 | 27811 |
| Candidozyma auris | SRR11092001 | SRR38908330 | 26797 | 27811 |
| Candidozyma auris | SRR11092001 | SRR38908334 | 26871 | 27811 |
| Candidozyma auris | SRR38908326 | SRR38908330 | 382 | 27811 |
| Candidozyma auris | SRR38908326 | SRR38908334 | 1590 | 27811 |
| Candidozyma auris | SRR38908330 | SRR38908334 | 1565 | 27811 |
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.