Samples analyzed50
Top species groups7
Total AMR hits24
Median N50126,932
1. Executive summary
The primary detected fungal species group was Clavispora lusitaniae. 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
Clavispora lusitaniae13
Candidozyma auris12
Nakaseomyces glabratus8
Pichia kudriavzevii6
Candida tropicalis5
Candida parapsilosis5
Candida albicans1
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 |
|---|---|---|---|---|---|---|---|---|---|---|
| SRR10967519 | missing | NA | Candida tropicalis | 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 |
| SRR11235409 | 2018-11-30 | 43.65 N 79.38 W | Candida albicans | High | Review | Review | 1 marker(s) | Excluded | Review | QUAST assembly QC; AMR marker detected |
| SRR11235422 | 2017-03-06 | 43.65 N 79.38 W | Nakaseomyces glabratus | High | Pass | Pass | 1 marker(s) | Review | Review | AMR marker detected |
| SRR11235424 | 2017-03-29 | 43.65 N 79.38 W | Nakaseomyces glabratus | High | Pass | Pass | 1 marker(s) | Review | Review | AMR marker detected |
| SRR11235425 | 2017-10-10 | 43.65 N 79.38 W | Nakaseomyces glabratus | High | Pass | Pass | 1 marker(s) | Review | Review | AMR marker detected |
| SRR11235426 | 2017-07-27 | 43.65 N 79.38 W | Nakaseomyces glabratus | High | Pass | Pass | 1 marker(s) | Review | Review | AMR marker detected |
| SRR11235427 | 2016-10-31 | 43.65 N 79.38 W | Nakaseomyces glabratus | High | Pass | Pass | 1 marker(s) | Review | Review | AMR marker detected |
| SRR11235428 | 2016-07-05 | 43.65 N 79.38 W | Nakaseomyces glabratus | High | Pass | Pass | 1 marker(s) | Review | Review | AMR marker detected |
| SRR11235429 | 2015-10-27 | 43.65 N 79.38 W | Nakaseomyces glabratus | High | Pass | Pass | 1 marker(s) | Review | Review | AMR marker detected |
| SRR11235430 | 2015-09-22 | 43.65 N 79.38 W | Nakaseomyces glabratus | High | Pass | Pass | 1 marker(s) | Review | Review | AMR marker detected |
| SRR12823762 | 2016 | NA | Candida tropicalis | High | Review | Review | No curated marker detected | Included / eligible | Review | QUAST assembly QC |
| SRR23951614 | 2015 | 43.64 N 72.25 W | Clavispora lusitaniae | 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 |
| SRR24123449 | 2020-10-08 | NA | Clavispora lusitaniae | 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 |
| SRR24123452 | 2020-10-07 | NA | Clavispora lusitaniae | 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 |
| SRR24123455 | 2020-12-16 | NA | Clavispora lusitaniae | 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 |
| SRR24123459 | 2020-10-16 | NA | Clavispora lusitaniae | 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 |
| SRR24123461 | 2020-10-13 | NA | Clavispora lusitaniae | 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 |
| SRR24123463 | 2020-10-12 | NA | Clavispora lusitaniae | 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 |
| SRR30781078 | 2020-07 | 25.38 N 68.37 E | Clavispora lusitaniae | 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 |
| SRR30781089 | 2020-10 | 25.38 N 68.37 E | Clavispora lusitaniae | 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 |
| SRR30781120 | 2020-10 | 32.08 N 72.67 E | Clavispora lusitaniae | 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 |
| SRR30781135 | 2023-03 | 30.2 N 71.47 E | Clavispora lusitaniae | High | Pass | Pass | 1 marker(s) | Excluded | Review | AMR marker detected |
| SRR30781188 | 2022-12 | 24.86 N 67.01 E | Clavispora lusitaniae | 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 |
| SRR30781189 | 2022-12 | 24.86 N 67.01 E | Clavispora lusitaniae | 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 |
| SRR35650155 | 2021 | NA | Candida tropicalis | 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 |
| SRR35650156 | 2021 | NA | Candida tropicalis | High | Review | Review | No curated marker detected | Included / eligible | Review | QUAST assembly QC |
| SRR35650157 | 2021 | NA | Candida tropicalis | High | Review | Review | No curated marker detected | Included / eligible | Review | QUAST assembly QC |
| SRR38394166 | NA | NA | Candida parapsilosis | High | Pass | Pass | 1 marker(s) | Excluded | Review | AMR marker detected |
| SRR38394168 | NA | NA | Candida parapsilosis | High | Pass | Pass | 1 marker(s) | Excluded | Review | AMR marker detected |
| SRR38394169 | NA | NA | Candida parapsilosis | High | Pass | Pass | 1 marker(s) | Excluded | Review | AMR marker detected |
| SRR38394173 | NA | NA | Candida parapsilosis | High | Pass | Pass | 1 marker(s) | Excluded | Review | AMR marker detected |
| SRR38394176 | NA | NA | Candida parapsilosis | High | Pass | Pass | 1 marker(s) | Excluded | Review | AMR marker detected |
| SRR38566159 | missing | NA | Pichia kudriavzevii | 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 |
| SRR38566164 | missing | NA | Pichia kudriavzevii | 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 |
| SRR38566207 | missing | NA | Pichia kudriavzevii | 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 |
| SRR38566258 | missing | NA | Pichia kudriavzevii | 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 |
| SRR38566259 | missing | NA | Pichia kudriavzevii | 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 |
| SRR38566263 | missing | NA | Pichia kudriavzevii | 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 |
| SRR38842632 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38842634 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38887223 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38906258 | 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 |
| SRR38906262 | 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 |
| SRR38906266 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38908327 | 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 |
| SRR38908328 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38908329 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38908333 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38908336 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
| SRR38908337 | NA | NA | Candidozyma auris | High | Pass | Pass | 1 marker(s) | Included / eligible | Review | AMR marker detected |
3. Surveillance metadata
| Sample | country | collection_date |
|---|---|---|
| SRR11235409 | Canada: Ontario | 2018-11-30 |
| SRR11235424 | Canada: Ontario | 2017-03-29 |
| SRR11235429 | Canada: Ontario | 2015-10-27 |
| SRR10967519 | missing | missing |
| SRR24123452 | USA: Minnesota | 2020-10-07 |
| SRR30781120 | Pakistan:Sargodha | 2020-10 |
| SRR30781189 | Pakistan:Karachi | 2022-12 |
| SRR35650155 | India:Jaipur | 2021 |
| SRR38842632 | ||
| SRR38842634 | ||
| SRR38908327 | ||
| SRR38908329 | ||
| SRR38908333 | ||
| SRR38566159 | missing | missing |
| SRR11235422 | Canada: Ontario | 2017-03-06 |
| SRR11235426 | Canada: Ontario | 2017-07-27 |
| SRR11235428 | Canada: Ontario | 2016-07-05 |
| SRR11235430 | Canada: Ontario | 2015-09-22 |
| SRR24123449 | USA: Minnesota | 2020-10-08 |
| SRR24123455 | USA: Minnesota | 2020-12-16 |
| SRR24123459 | USA: Minnesota | 2020-10-16 |
| SRR24123461 | USA: Minnesota | 2020-10-13 |
| SRR24123463 | USA: Minnesota | 2020-10-12 |
| SRR30781188 | Pakistan:Karachi | 2022-12 |
| SRR35650156 | India:Jaipur | 2021 |
| SRR35650157 | India:Jaipur | 2021 |
| SRR38887223 | ||
| SRR38908328 | ||
| SRR38908336 | ||
| SRR38394166 | ||
| SRR38394169 | ||
| SRR38394176 | ||
| SRR38566258 | missing | missing |
| SRR38566263 | missing | missing |
| SRR11235425 | Canada: Ontario | 2017-10-10 |
| SRR11235427 | Canada: Ontario | 2016-10-31 |
| SRR12823762 | Spain | 2016 |
| SRR23951614 | USA: Hanover, NH | 2015 |
| SRR30781078 | Pakistan:Hyderabad | 2020-07 |
| SRR30781089 | Pakistan:Hyderabad | 2020-10 |
| SRR30781135 | Pakistan:Multan | 2023-03 |
| SRR38394168 | ||
| SRR38394173 | ||
| SRR38566164 | missing | missing |
| SRR38566207 | missing | missing |
| SRR38566259 | missing | missing |
| SRR38906258 | ||
| SRR38906262 | ||
| SRR38906266 | ||
| SRR38908337 |
4. Sample-level surveillance summary
SRR10967519
Candida tropicalis Ready for surveillance interpretation
Species reads99.92%
Contigs783
N5070,387
GC (%)33.03
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 (5 samples)
SRR11235409
Candida albicans Review
Species reads98.89%
Contigs4,260
N509,806
GC (%)33.94
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.
SRR11235422
Nakaseomyces glabratus Review
Species reads100.00%
Contigs889
N5051,761
GC (%)38.73
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.
SRR11235424
Nakaseomyces glabratus Review
Species reads99.99%
Contigs1,130
N5036,125
GC (%)38.79
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.
SRR11235425
Nakaseomyces glabratus Review
Species reads99.99%
Contigs1,123
N5037,964
GC (%)38.76
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.
SRR11235426
Nakaseomyces glabratus Review
Species reads99.99%
Contigs1,466
N5022,403
GC (%)38.74
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.
SRR11235427
Nakaseomyces glabratus Review
Species reads99.99%
Contigs1,160
N5036,886
GC (%)38.80
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.
SRR11235428
Nakaseomyces glabratus Review
Species reads99.99%
Contigs1,309
N5032,230
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.
SRR11235429
Nakaseomyces glabratus Review
Species reads99.99%
Contigs1,180
N5037,394
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.
SRR11235430
Nakaseomyces glabratus Review
Species reads99.99%
Contigs1,708
N5043,764
GC (%)38.85
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.
SRR12823762
Candida tropicalis Review
Species reads99.75%
Contigs13,125
N502,245
GC (%)33.37
No curated genomic AMR marker detected — not susceptible Species confidence: High Phylogeny: Included / eligible
Interpretation: QUAST assembly QC. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (5 samples)
SRR23951614
Clavispora lusitaniae Ready for surveillance interpretation
Species reads99.92%
Contigs246
N50151,973
GC (%)44.49
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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR23951614:variant_calling_failed,SRR24123449:variant_calling_failed,SRR24123452:variant_calling_failed,SRR24123455:variant_calling_failed,SRR24123459:variant_calling_failed,SRR24123461:variant_calling_failed,SRR24123463:variant_calling_failed,SRR30781078:variant_calling_failed,SRR30781089:variant_calling_failed,SRR30781120:variant_calling_failed,SRR30781135:variant_calling_failed,SRR30781188:variant_calling_failed,SRR30781189:variant_calling_failed
SRR24123449
Clavispora lusitaniae Ready for surveillance interpretation
Species reads99.91%
Contigs129
N50308,077
GC (%)44.48
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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR23951614:variant_calling_failed,SRR24123449:variant_calling_failed,SRR24123452:variant_calling_failed,SRR24123455:variant_calling_failed,SRR24123459:variant_calling_failed,SRR24123461:variant_calling_failed,SRR24123463:variant_calling_failed,SRR30781078:variant_calling_failed,SRR30781089:variant_calling_failed,SRR30781120:variant_calling_failed,SRR30781135:variant_calling_failed,SRR30781188:variant_calling_failed,SRR30781189:variant_calling_failed
SRR24123452
Clavispora lusitaniae Ready for surveillance interpretation
Species reads99.90%
Contigs125
N50254,386
GC (%)44.48
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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR23951614:variant_calling_failed,SRR24123449:variant_calling_failed,SRR24123452:variant_calling_failed,SRR24123455:variant_calling_failed,SRR24123459:variant_calling_failed,SRR24123461:variant_calling_failed,SRR24123463:variant_calling_failed,SRR30781078:variant_calling_failed,SRR30781089:variant_calling_failed,SRR30781120:variant_calling_failed,SRR30781135:variant_calling_failed,SRR30781188:variant_calling_failed,SRR30781189:variant_calling_failed
SRR24123455
Clavispora lusitaniae Ready for surveillance interpretation
Species reads99.93%
Contigs91
N50405,269
GC (%)44.48
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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR23951614:variant_calling_failed,SRR24123449:variant_calling_failed,SRR24123452:variant_calling_failed,SRR24123455:variant_calling_failed,SRR24123459:variant_calling_failed,SRR24123461:variant_calling_failed,SRR24123463:variant_calling_failed,SRR30781078:variant_calling_failed,SRR30781089:variant_calling_failed,SRR30781120:variant_calling_failed,SRR30781135:variant_calling_failed,SRR30781188:variant_calling_failed,SRR30781189:variant_calling_failed
SRR24123459
Clavispora lusitaniae Ready for surveillance interpretation
Species reads99.89%
Contigs121
N50243,251
GC (%)44.48
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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR23951614:variant_calling_failed,SRR24123449:variant_calling_failed,SRR24123452:variant_calling_failed,SRR24123455:variant_calling_failed,SRR24123459:variant_calling_failed,SRR24123461:variant_calling_failed,SRR24123463:variant_calling_failed,SRR30781078:variant_calling_failed,SRR30781089:variant_calling_failed,SRR30781120:variant_calling_failed,SRR30781135:variant_calling_failed,SRR30781188:variant_calling_failed,SRR30781189:variant_calling_failed
SRR24123461
Clavispora lusitaniae Ready for surveillance interpretation
Species reads99.90%
Contigs118
N50232,565
GC (%)44.48
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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR23951614:variant_calling_failed,SRR24123449:variant_calling_failed,SRR24123452:variant_calling_failed,SRR24123455:variant_calling_failed,SRR24123459:variant_calling_failed,SRR24123461:variant_calling_failed,SRR24123463:variant_calling_failed,SRR30781078:variant_calling_failed,SRR30781089:variant_calling_failed,SRR30781120:variant_calling_failed,SRR30781135:variant_calling_failed,SRR30781188:variant_calling_failed,SRR30781189:variant_calling_failed
SRR24123463
Clavispora lusitaniae Ready for surveillance interpretation
Species reads99.91%
Contigs117
N50294,188
GC (%)44.48
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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR23951614:variant_calling_failed,SRR24123449:variant_calling_failed,SRR24123452:variant_calling_failed,SRR24123455:variant_calling_failed,SRR24123459:variant_calling_failed,SRR24123461:variant_calling_failed,SRR24123463:variant_calling_failed,SRR30781078:variant_calling_failed,SRR30781089:variant_calling_failed,SRR30781120:variant_calling_failed,SRR30781135:variant_calling_failed,SRR30781188:variant_calling_failed,SRR30781189:variant_calling_failed
SRR30781078
Clavispora lusitaniae Ready for surveillance interpretation
Species reads99.97%
Contigs244
N50110,023
GC (%)44.47
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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR23951614:variant_calling_failed,SRR24123449:variant_calling_failed,SRR24123452:variant_calling_failed,SRR24123455:variant_calling_failed,SRR24123459:variant_calling_failed,SRR24123461:variant_calling_failed,SRR24123463:variant_calling_failed,SRR30781078:variant_calling_failed,SRR30781089:variant_calling_failed,SRR30781120:variant_calling_failed,SRR30781135:variant_calling_failed,SRR30781188:variant_calling_failed,SRR30781189:variant_calling_failed
SRR30781089
Clavispora lusitaniae Ready for surveillance interpretation
Species reads99.97%
Contigs211
N50124,527
GC (%)44.48
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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR23951614:variant_calling_failed,SRR24123449:variant_calling_failed,SRR24123452:variant_calling_failed,SRR24123455:variant_calling_failed,SRR24123459:variant_calling_failed,SRR24123461:variant_calling_failed,SRR24123463:variant_calling_failed,SRR30781078:variant_calling_failed,SRR30781089:variant_calling_failed,SRR30781120:variant_calling_failed,SRR30781135:variant_calling_failed,SRR30781188:variant_calling_failed,SRR30781189:variant_calling_failed
SRR30781120
Clavispora lusitaniae Ready for surveillance interpretation
Species reads99.96%
Contigs197
N50155,295
GC (%)44.47
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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR23951614:variant_calling_failed,SRR24123449:variant_calling_failed,SRR24123452:variant_calling_failed,SRR24123455:variant_calling_failed,SRR24123459:variant_calling_failed,SRR24123461:variant_calling_failed,SRR24123463:variant_calling_failed,SRR30781078:variant_calling_failed,SRR30781089:variant_calling_failed,SRR30781120:variant_calling_failed,SRR30781135:variant_calling_failed,SRR30781188:variant_calling_failed,SRR30781189:variant_calling_failed
SRR30781135
Clavispora lusitaniae Review
Species reads99.83%
Contigs109
N50356,902
GC (%)44.48
1 AMR hit(s) Species confidence: High Phylogeny: Excluded
Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR23951614:variant_calling_failed,SRR24123449:variant_calling_failed,SRR24123452:variant_calling_failed,SRR24123455:variant_calling_failed,SRR24123459:variant_calling_failed,SRR24123461:variant_calling_failed,SRR24123463:variant_calling_failed,SRR30781078:variant_calling_failed,SRR30781089:variant_calling_failed,SRR30781120:variant_calling_failed,SRR30781135:variant_calling_failed,SRR30781188:variant_calling_failed,SRR30781189:variant_calling_failed
SRR30781188
Clavispora lusitaniae Ready for surveillance interpretation
Species reads99.85%
Contigs120
N50332,841
GC (%)44.50
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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR23951614:variant_calling_failed,SRR24123449:variant_calling_failed,SRR24123452:variant_calling_failed,SRR24123455:variant_calling_failed,SRR24123459:variant_calling_failed,SRR24123461:variant_calling_failed,SRR24123463:variant_calling_failed,SRR30781078:variant_calling_failed,SRR30781089:variant_calling_failed,SRR30781120:variant_calling_failed,SRR30781135:variant_calling_failed,SRR30781188:variant_calling_failed,SRR30781189:variant_calling_failed
SRR30781189
Clavispora lusitaniae Ready for surveillance interpretation
Species reads99.85%
Contigs176
N50183,855
GC (%)44.50
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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR23951614:variant_calling_failed,SRR24123449:variant_calling_failed,SRR24123452:variant_calling_failed,SRR24123455:variant_calling_failed,SRR24123459:variant_calling_failed,SRR24123461:variant_calling_failed,SRR24123463:variant_calling_failed,SRR30781078:variant_calling_failed,SRR30781089:variant_calling_failed,SRR30781120:variant_calling_failed,SRR30781135:variant_calling_failed,SRR30781188:variant_calling_failed,SRR30781189:variant_calling_failed
SRR35650155
Candida tropicalis Ready for surveillance interpretation
Species reads99.95%
Contigs923
N5061,509
GC (%)33.05
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 (5 samples)
SRR35650156
Candida tropicalis Review
Species reads99.95%
Contigs3,748
N5042,858
GC (%)39.04
No curated genomic AMR marker detected — not susceptible Species confidence: High Phylogeny: Included / eligible
Interpretation: QUAST assembly QC. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (5 samples)
SRR35650157
Candida tropicalis Review
Species reads99.95%
Contigs4,002
N5044,661
GC (%)37.65
No curated genomic AMR marker detected — not susceptible Species confidence: High Phylogeny: Included / eligible
Interpretation: QUAST assembly QC. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (5 samples)
SRR38394166
Candida parapsilosis Review
Species reads99.99%
Contigs408
N50118,157
GC (%)38.66
1 AMR hit(s) Species confidence: High Phylogeny: Excluded
Interpretation: AMR marker detected. 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.
SRR38394168
Candida parapsilosis Review
Species reads99.99%
Contigs412
N50108,682
GC (%)38.66
1 AMR hit(s) Species confidence: High Phylogeny: Excluded
Interpretation: AMR marker detected. 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.
SRR38394169
Candida parapsilosis Review
Species reads100.00%
Contigs378
N50110,492
GC (%)38.65
1 AMR hit(s) Species confidence: High Phylogeny: Excluded
Interpretation: AMR marker detected. 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.
SRR38394173
Candida parapsilosis Review
Species reads99.99%
Contigs405
N50108,680
GC (%)38.65
1 AMR hit(s) Species confidence: High Phylogeny: Excluded
Interpretation: AMR marker detected. 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.
SRR38394176
Candida parapsilosis Review
Species reads100.00%
Contigs412
N5098,593
GC (%)38.65
1 AMR hit(s) Species confidence: High Phylogeny: Excluded
Interpretation: AMR marker detected. 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.
SRR38566159
Pichia kudriavzevii Ready for surveillance interpretation
Species reads99.86%
Contigs331
N50139,390
GC (%)38.27
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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR38566159:variant_calling_failed,SRR38566164:variant_calling_failed,SRR38566207:variant_calling_failed,SRR38566258:variant_calling_failed,SRR38566259:variant_calling_failed,SRR38566263:variant_calling_failed
SRR38566164
Pichia kudriavzevii Ready for surveillance interpretation
Species reads99.83%
Contigs353
N50129,338
GC (%)38.27
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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR38566159:variant_calling_failed,SRR38566164:variant_calling_failed,SRR38566207:variant_calling_failed,SRR38566258:variant_calling_failed,SRR38566259:variant_calling_failed,SRR38566263:variant_calling_failed
SRR38566207
Pichia kudriavzevii Ready for surveillance interpretation
Species reads99.86%
Contigs338
N50123,479
GC (%)38.27
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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR38566159:variant_calling_failed,SRR38566164:variant_calling_failed,SRR38566207:variant_calling_failed,SRR38566258:variant_calling_failed,SRR38566259:variant_calling_failed,SRR38566263:variant_calling_failed
SRR38566258
Pichia kudriavzevii Ready for surveillance interpretation
Species reads99.78%
Contigs377
N50141,968
GC (%)38.27
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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR38566159:variant_calling_failed,SRR38566164:variant_calling_failed,SRR38566207:variant_calling_failed,SRR38566258:variant_calling_failed,SRR38566259:variant_calling_failed,SRR38566263:variant_calling_failed
SRR38566259
Pichia kudriavzevii Ready for surveillance interpretation
Species reads99.87%
Contigs367
N50132,382
GC (%)38.27
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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR38566159:variant_calling_failed,SRR38566164:variant_calling_failed,SRR38566207:variant_calling_failed,SRR38566258:variant_calling_failed,SRR38566259:variant_calling_failed,SRR38566263:variant_calling_failed
SRR38566263
Pichia kudriavzevii Ready for surveillance interpretation
Species reads99.39%
Contigs461
N50119,406
GC (%)38.30
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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR38566159:variant_calling_failed,SRR38566164:variant_calling_failed,SRR38566207:variant_calling_failed,SRR38566258:variant_calling_failed,SRR38566259:variant_calling_failed,SRR38566263:variant_calling_failed
SRR38842632
Candidozyma auris Review
Species reads99.31%
Contigs1,112
N5024,296
GC (%)44.89
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)
SRR38842634
Candidozyma auris Review
Species reads99.62%
Contigs1,120
N5024,271
GC (%)44.86
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)
SRR38887223
Candidozyma auris Review
Species reads99.35%
Contigs108
N50282,927
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)
SRR38906258
Candidozyma auris Ready for surveillance interpretation
Species reads99.53%
Contigs101
N50248,883
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 (12 samples)
SRR38906262
Candidozyma auris Ready for surveillance interpretation
Species reads99.44%
Contigs93
N50230,926
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 (12 samples)
SRR38906266
Candidozyma auris Review
Species reads99.41%
Contigs82
N50337,956
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)
SRR38908327
Candidozyma auris Ready for surveillance interpretation
Species reads99.27%
Contigs139
N50164,662
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 (12 samples)
SRR38908328
Candidozyma auris Review
Species reads99.47%
Contigs128
N50201,158
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)
SRR38908329
Candidozyma auris Review
Species reads99.38%
Contigs129
N50241,241
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)
SRR38908333
Candidozyma auris Review
Species reads99.35%
Contigs117
N50214,791
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)
SRR38908336
Candidozyma auris Review
Species reads99.20%
Contigs120
N50201,103
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)
SRR38908337
Candidozyma auris Review
Species reads99.20%
Contigs106
N50267,970
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)
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 |
|---|---|---|---|---|---|---|
| SRR10967519 | Candida tropicalis | 99.92% | 2,245,401 | 2,245,401 | 5482 | Bracken species-level abundance |
| SRR11235409 | Candida albicans | 98.89% | 2,015,149 | 2,015,149 | 5476 | Bracken species-level abundance |
| SRR11235422 | Nakaseomyces glabratus | 100.00% | 2,486,966 | 2,486,966 | 5478 | Bracken species-level abundance |
| SRR11235424 | Nakaseomyces glabratus | 99.99% | 1,798,369 | 1,798,369 | 5478 | Bracken species-level abundance |
| SRR11235425 | Nakaseomyces glabratus | 99.99% | 1,730,018 | 1,730,018 | 5478 | Bracken species-level abundance |
| SRR11235426 | Nakaseomyces glabratus | 99.99% | 980,802 | 980,802 | 5478 | Bracken species-level abundance |
| SRR11235427 | Nakaseomyces glabratus | 99.99% | 2,268,580 | 2,268,580 | 5478 | Bracken species-level abundance |
| SRR11235428 | Nakaseomyces glabratus | 99.99% | 1,767,581 | 1,767,581 | 5478 | Bracken species-level abundance |
| SRR11235429 | Nakaseomyces glabratus | 99.99% | 1,940,364 | 1,940,364 | 5478 | Bracken species-level abundance |
| SRR11235430 | Nakaseomyces glabratus | 99.99% | 1,896,470 | 1,896,470 | 5478 | Bracken species-level abundance |
| SRR12823762 | Candida tropicalis | 99.75% | 646,131 | 646,131 | 5482 | Bracken species-level abundance |
| SRR23951614 | Clavispora lusitaniae | 99.92% | 2,736,149 | 2,736,149 | 36911 | Bracken species-level abundance |
| SRR24123449 | Clavispora lusitaniae | 99.91% | 3,891,017 | 3,891,017 | 36911 | Bracken species-level abundance |
| SRR24123452 | Clavispora lusitaniae | 99.90% | 3,480,773 | 3,480,773 | 36911 | Bracken species-level abundance |
| SRR24123455 | Clavispora lusitaniae | 99.93% | 4,515,686 | 4,515,686 | 36911 | Bracken species-level abundance |
| SRR24123459 | Clavispora lusitaniae | 99.89% | 3,899,805 | 3,899,805 | 36911 | Bracken species-level abundance |
| SRR24123461 | Clavispora lusitaniae | 99.90% | 3,309,226 | 3,309,226 | 36911 | Bracken species-level abundance |
| SRR24123463 | Clavispora lusitaniae | 99.91% | 3,966,041 | 3,966,041 | 36911 | Bracken species-level abundance |
| SRR30781078 | Clavispora lusitaniae | 99.97% | 2,715,450 | 2,715,450 | 36911 | Bracken species-level abundance |
| SRR30781089 | Clavispora lusitaniae | 99.97% | 4,164,138 | 4,164,138 | 36911 | Bracken species-level abundance |
| SRR30781120 | Clavispora lusitaniae | 99.96% | 2,925,472 | 2,925,472 | 36911 | Bracken species-level abundance |
| SRR30781135 | Clavispora lusitaniae | 99.83% | 4,454,973 | 4,454,973 | 36911 | Bracken species-level abundance |
| SRR30781188 | Clavispora lusitaniae | 99.85% | 2,540,913 | 2,540,913 | 36911 | Bracken species-level abundance |
| SRR30781189 | Clavispora lusitaniae | 99.85% | 1,439,901 | 1,439,901 | 36911 | Bracken species-level abundance |
| SRR35650155 | Candida tropicalis | 99.95% | 6,133,889 | 6,133,889 | 5482 | Bracken species-level abundance |
| SRR35650156 | Candida tropicalis | 99.95% | 4,818,099 | 4,818,099 | 5482 | Bracken species-level abundance |
| SRR35650157 | Candida tropicalis | 99.95% | 5,537,486 | 5,537,486 | 5482 | Bracken species-level abundance |
| SRR38394166 | Candida parapsilosis | 99.99% | 5,121,188 | 5,121,188 | 5480 | Bracken species-level abundance |
| SRR38394168 | Candida parapsilosis | 99.99% | 7,921,555 | 7,921,555 | 5480 | Bracken species-level abundance |
| SRR38394169 | Candida parapsilosis | 100.00% | 6,127,464 | 6,127,464 | 5480 | Bracken species-level abundance |
| SRR38394173 | Candida parapsilosis | 99.99% | 5,148,893 | 5,148,893 | 5480 | Bracken species-level abundance |
| SRR38394176 | Candida parapsilosis | 100.00% | 3,639,866 | 3,639,866 | 5480 | Bracken species-level abundance |
| SRR38566159 | Pichia kudriavzevii | 99.86% | 2,117,429 | 2,117,429 | 4909 | Bracken species-level abundance |
| SRR38566164 | Pichia kudriavzevii | 99.83% | 2,587,191 | 2,587,191 | 4909 | Bracken species-level abundance |
| SRR38566207 | Pichia kudriavzevii | 99.86% | 2,664,054 | 2,664,054 | 4909 | Bracken species-level abundance |
| SRR38566258 | Pichia kudriavzevii | 99.78% | 4,070,196 | 4,070,196 | 4909 | Bracken species-level abundance |
| SRR38566259 | Pichia kudriavzevii | 99.87% | 6,220,119 | 6,220,119 | 4909 | Bracken species-level abundance |
| SRR38566263 | Pichia kudriavzevii | 99.39% | 5,596,719 | 5,596,719 | 4909 | Bracken species-level abundance |
| SRR38842632 | Candidozyma auris | 99.31% | 1,802,175 | 1,802,175 | 498019 | Bracken species-level abundance |
| SRR38842634 | Candidozyma auris | 99.62% | 1,527,796 | 1,527,796 | 498019 | Bracken species-level abundance |
| SRR38887223 | Candidozyma auris | 99.35% | 4,221,880 | 4,221,880 | 498019 | Bracken species-level abundance |
| SRR38906258 | Candidozyma auris | 99.53% | 2,574,438 | 2,574,438 | 498019 | Bracken species-level abundance |
| SRR38906262 | Candidozyma auris | 99.44% | 2,145,012 | 2,145,012 | 498019 | Bracken species-level abundance |
| SRR38906266 | Candidozyma auris | 99.41% | 2,962,879 | 2,962,879 | 498019 | Bracken species-level abundance |
| SRR38908327 | Candidozyma auris | 99.27% | 1,291,393 | 1,291,393 | 498019 | Bracken species-level abundance |
| SRR38908328 | Candidozyma auris | 99.47% | 1,312,195 | 1,312,195 | 498019 | Bracken species-level abundance |
| SRR38908329 | Candidozyma auris | 99.38% | 1,310,216 | 1,310,216 | 498019 | Bracken species-level abundance |
| SRR38908333 | Candidozyma auris | 99.35% | 1,269,325 | 1,269,325 | 498019 | Bracken species-level abundance |
| SRR38908336 | Candidozyma auris | 99.20% | 1,262,841 | 1,262,841 | 498019 | Bracken species-level abundance |
| SRR38908337 | Candidozyma auris | 99.20% | 1,346,332 | 1,346,332 | 498019 | Bracken species-level abundance |
6. MEGAHIT assembly summary
| Sample | contigs | Total bp | N50 | Largest contig |
|---|---|---|---|---|
| SRR10967519 | 783 | 14,547,377 | 70,387 | 274,961 |
| SRR11235409 | 4,260 | 14,866,017 | 9,806 | 74,958 |
| SRR11235422 | 889 | 12,406,596 | 51,761 | 245,683 |
| SRR11235424 | 1,130 | 12,453,228 | 36,125 | 151,164 |
| SRR11235425 | 1,123 | 12,452,016 | 37,964 | 126,793 |
| SRR11235426 | 1,466 | 12,417,104 | 22,403 | 76,065 |
| SRR11235427 | 1,160 | 12,454,115 | 36,886 | 144,809 |
| SRR11235428 | 1,309 | 12,464,248 | 32,230 | 114,568 |
| SRR11235429 | 1,180 | 12,477,340 | 37,394 | 151,237 |
| SRR11235430 | 1,708 | 12,955,037 | 43,764 | 187,392 |
| SRR12823762 | 13,125 | 22,734,561 | 2,245 | 60,447 |
| SRR23951614 | 246 | 12,066,731 | 151,973 | 555,387 |
| SRR24123449 | 129 | 12,021,032 | 308,077 | 555,823 |
| SRR24123452 | 125 | 12,022,620 | 254,386 | 761,890 |
| SRR24123455 | 91 | 12,032,189 | 405,269 | 702,787 |
| SRR24123459 | 121 | 12,020,972 | 243,251 | 682,095 |
| SRR24123461 | 118 | 12,021,806 | 232,565 | 563,905 |
| SRR24123463 | 117 | 12,022,753 | 294,188 | 585,635 |
| SRR30781078 | 244 | 12,055,837 | 110,023 | 302,748 |
| SRR30781089 | 211 | 11,962,891 | 124,527 | 522,509 |
| SRR30781120 | 197 | 12,012,346 | 155,295 | 496,760 |
| SRR30781135 | 109 | 12,024,865 | 356,902 | 1,070,351 |
| SRR30781188 | 120 | 12,004,815 | 332,841 | 591,408 |
| SRR30781189 | 176 | 12,000,418 | 183,855 | 564,176 |
| SRR35650155 | 923 | 14,582,158 | 61,509 | 279,335 |
| SRR35650156 | 3,748 | 18,893,551 | 42,858 | 241,006 |
| SRR35650157 | 4,002 | 17,739,056 | 44,661 | 304,022 |
| SRR38394166 | 408 | 12,927,998 | 118,157 | 324,348 |
| SRR38394168 | 412 | 12,927,292 | 108,682 | 315,940 |
| SRR38394169 | 378 | 12,917,119 | 110,492 | 324,206 |
| SRR38394173 | 405 | 12,924,249 | 108,680 | 306,523 |
| SRR38394176 | 412 | 12,931,867 | 98,593 | 315,884 |
| SRR38566159 | 331 | 10,722,047 | 139,390 | 543,699 |
| SRR38566164 | 353 | 10,737,259 | 129,338 | 543,792 |
| SRR38566207 | 338 | 10,729,778 | 123,479 | 543,725 |
| SRR38566258 | 377 | 10,757,572 | 141,968 | 543,700 |
| SRR38566259 | 367 | 10,751,121 | 132,382 | 564,873 |
| SRR38566263 | 461 | 10,843,815 | 119,406 | 500,867 |
| SRR38842632 | 1,112 | 12,653,737 | 24,296 | 90,978 |
| SRR38842634 | 1,120 | 12,675,806 | 24,271 | 86,820 |
| SRR38887223 | 108 | 12,343,501 | 282,927 | 904,008 |
| SRR38906258 | 101 | 12,307,824 | 248,883 | 521,062 |
| SRR38906262 | 93 | 12,309,419 | 230,926 | 737,554 |
| SRR38906266 | 82 | 12,358,283 | 337,956 | 1,155,126 |
| SRR38908327 | 139 | 12,315,028 | 164,662 | 492,602 |
| SRR38908328 | 128 | 12,362,743 | 201,158 | 1,051,533 |
| SRR38908329 | 129 | 12,365,340 | 241,241 | 544,377 |
| SRR38908333 | 117 | 12,339,786 | 214,791 | 587,368 |
| SRR38908336 | 120 | 12,344,434 | 201,103 | 662,866 |
| SRR38908337 | 106 | 12,342,448 | 267,970 | 759,589 |
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 |
|---|---|---|---|---|---|
| SRR10967519 | 783 | 274,961 | 14,547,377 | 33.03 | 70,387 |
| SRR11235409 | 4,260 | 74,958 | 14,866,017 | 33.94 | 9,806 |
| SRR11235422 | 889 | 245,683 | 12,406,596 | 38.73 | 51,761 |
| SRR11235424 | 1,130 | 151,164 | 12,453,228 | 38.79 | 36,125 |
| SRR11235425 | 1,123 | 126,793 | 12,452,016 | 38.76 | 37,964 |
| SRR11235426 | 1,466 | 76,065 | 12,417,104 | 38.74 | 22,403 |
| SRR11235427 | 1,160 | 144,809 | 12,454,115 | 38.80 | 36,886 |
| SRR11235428 | 1,309 | 114,568 | 12,464,248 | 38.83 | 32,230 |
| SRR11235429 | 1,180 | 151,237 | 12,477,340 | 38.83 | 37,394 |
| SRR11235430 | 1,708 | 187,392 | 12,955,037 | 38.85 | 43,764 |
| SRR12823762 | 13,125 | 60,447 | 22,734,561 | 33.37 | 2,245 |
| SRR23951614 | 246 | 555,387 | 12,066,731 | 44.49 | 151,973 |
| SRR24123449 | 129 | 555,823 | 12,021,032 | 44.48 | 308,077 |
| SRR24123452 | 125 | 761,890 | 12,022,620 | 44.48 | 254,386 |
| SRR24123455 | 91 | 702,787 | 12,032,189 | 44.48 | 405,269 |
| SRR24123459 | 121 | 682,095 | 12,020,972 | 44.48 | 243,251 |
| SRR24123461 | 118 | 563,905 | 12,021,806 | 44.48 | 232,565 |
| SRR24123463 | 117 | 585,635 | 12,022,753 | 44.48 | 294,188 |
| SRR30781078 | 244 | 302,748 | 12,055,837 | 44.47 | 110,023 |
| SRR30781089 | 211 | 522,509 | 11,962,891 | 44.48 | 124,527 |
| SRR30781120 | 197 | 496,760 | 12,012,346 | 44.47 | 155,295 |
| SRR30781135 | 109 | 1,070,351 | 12,024,865 | 44.48 | 356,902 |
| SRR30781188 | 120 | 591,408 | 12,004,815 | 44.50 | 332,841 |
| SRR30781189 | 176 | 564,176 | 12,000,418 | 44.50 | 183,855 |
| SRR35650155 | 923 | 279,335 | 14,582,158 | 33.05 | 61,509 |
| SRR35650156 | 3,748 | 241,006 | 18,893,551 | 39.04 | 42,858 |
| SRR35650157 | 4,002 | 304,022 | 17,739,056 | 37.65 | 44,661 |
| SRR38394166 | 408 | 324,348 | 12,927,998 | 38.66 | 118,157 |
| SRR38394168 | 412 | 315,940 | 12,927,292 | 38.66 | 108,682 |
| SRR38394169 | 378 | 324,206 | 12,917,119 | 38.65 | 110,492 |
| SRR38394173 | 405 | 306,523 | 12,924,249 | 38.65 | 108,680 |
| SRR38394176 | 412 | 315,884 | 12,931,867 | 38.65 | 98,593 |
| SRR38566159 | 331 | 543,699 | 10,722,047 | 38.27 | 139,390 |
| SRR38566164 | 353 | 543,792 | 10,737,259 | 38.27 | 129,338 |
| SRR38566207 | 338 | 543,725 | 10,729,778 | 38.27 | 123,479 |
| SRR38566258 | 377 | 543,700 | 10,757,572 | 38.27 | 141,968 |
| SRR38566259 | 367 | 564,873 | 10,751,121 | 38.27 | 132,382 |
| SRR38566263 | 461 | 500,867 | 10,843,815 | 38.30 | 119,406 |
| SRR38842632 | 1,112 | 90,978 | 12,653,737 | 44.89 | 24,296 |
| SRR38842634 | 1,120 | 86,820 | 12,675,806 | 44.86 | 24,271 |
| SRR38887223 | 108 | 904,008 | 12,343,501 | 45.14 | 282,927 |
| SRR38906258 | 101 | 521,062 | 12,307,824 | 45.15 | 248,883 |
| SRR38906262 | 93 | 737,554 | 12,309,419 | 45.15 | 230,926 |
| SRR38906266 | 82 | 1,155,126 | 12,358,283 | 45.14 | 337,956 |
| SRR38908327 | 139 | 492,602 | 12,315,028 | 45.15 | 164,662 |
| SRR38908328 | 128 | 1,051,533 | 12,362,743 | 45.14 | 201,158 |
| SRR38908329 | 129 | 544,377 | 12,365,340 | 45.14 | 241,241 |
| SRR38908333 | 117 | 587,368 | 12,339,786 | 45.14 | 214,791 |
| SRR38908336 | 120 | 662,866 | 12,344,434 | 45.14 | 201,103 |
| SRR38908337 | 106 | 759,589 | 12,342,448 | 45.14 | 267,970 |
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 |
|---|---|---|---|---|---|---|---|---|
| SRR10967519 | 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/SRR10967519.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR10967519.contigs |
| SRR11235409 | Candida albicans | azole | fluconazole/other azoles | Cyp51 | D116E | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 D116E (FungAMR MUTATION). Drug evidence from ChroQueTas: Clotrimazole(3/NA),Fluconazole(3/-1),Isavuconazole(3/NA),Itraconazole(8/-1),Posaconazole(NA/-1),Voriconazole(NA/-1). Source: amr_out/SRR11235409.ChroQueTas/SRR11235409.contigs.ChroQueTaS.Cyp51.1.tsv:116 |
| SRR11235422 | Nakaseomyces glabratus | antifungal | species-aware antifungal panel | Cdr1 | H58Y | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cdr1 H58Y (FungAMR MUTATION). Drug evidence from ChroQueTas: Various(NA/-8). Source: amr_out/SRR11235422.ChroQueTas/SRR11235422.contigs.ChroQueTaS.Cdr1.1.tsv:58 |
| SRR11235424 | 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/SRR11235424.ChroQueTas/SRR11235424.contigs.ChroQueTaS.Ben1.1.tsv:254 |
| SRR11235425 | Nakaseomyces glabratus | antifungal | species-aware antifungal panel | Erg2 | I207V | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Erg2 I207V (FungAMR MUTATION). Drug evidence from ChroQueTas: Various(NA/-8). Source: amr_out/SRR11235425.ChroQueTas/SRR11235425.contigs.ChroQueTaS.Erg2.1.tsv:207 |
| SRR11235426 | Nakaseomyces glabratus | antifungal | species-aware antifungal panel | Erg2 | I207V | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Erg2 I207V (FungAMR MUTATION). Drug evidence from ChroQueTas: Various(NA/-8). Source: amr_out/SRR11235426.ChroQueTas/SRR11235426.contigs.ChroQueTaS.Erg2.1.tsv:207 |
| SRR11235427 | Nakaseomyces glabratus | antifungal | species-aware antifungal panel | Erg2 | I207V | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Erg2 I207V (FungAMR MUTATION). Drug evidence from ChroQueTas: Various(NA/-8). Source: amr_out/SRR11235427.ChroQueTas/SRR11235427.contigs.ChroQueTaS.Erg2.1.tsv:207 |
| SRR11235428 | Nakaseomyces glabratus | antifungal | species-aware antifungal panel | Erg2 | I207V | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Erg2 I207V (FungAMR MUTATION). Drug evidence from ChroQueTas: Various(NA/-8). Source: amr_out/SRR11235428.ChroQueTas/SRR11235428.contigs.ChroQueTaS.Erg2.1.tsv:207 |
| SRR11235429 | Nakaseomyces glabratus | antifungal | species-aware antifungal panel | Erg2 | I207V | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Erg2 I207V (FungAMR MUTATION). Drug evidence from ChroQueTas: Various(NA/-8). Source: amr_out/SRR11235429.ChroQueTas/SRR11235429.contigs.ChroQueTaS.Erg2.1.tsv:207 |
| SRR11235430 | Nakaseomyces glabratus | antifungal | species-aware antifungal panel | Erg2 | I207V | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Erg2 I207V (FungAMR MUTATION). Drug evidence from ChroQueTas: Various(NA/-8). Source: amr_out/SRR11235430.ChroQueTas/SRR11235430.contigs.ChroQueTaS.Erg2.1.tsv:207 |
| SRR12823762 | 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/SRR12823762.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR12823762.contigs |
| SRR23951614 | 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/SRR23951614.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR23951614.contigs |
| SRR24123449 | 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/SRR24123449.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR24123449.contigs |
| SRR24123452 | 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/SRR24123452.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR24123452.contigs |
| SRR24123455 | 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/SRR24123455.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR24123455.contigs |
| SRR24123459 | 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/SRR24123459.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR24123459.contigs |
| SRR24123461 | 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/SRR24123461.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR24123461.contigs |
| SRR24123463 | 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/SRR24123463.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR24123463.contigs |
| SRR30781078 | 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/SRR30781078.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR30781078.contigs |
| SRR30781089 | 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/SRR30781089.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR30781089.contigs |
| SRR30781120 | 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/SRR30781120.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR30781120.contigs |
| SRR30781135 | Clavispora lusitaniae | flucytosine | flucytosine | Fcy1 | M9T | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Fcy1 M9T (FungAMR MUTATION). Drug evidence from ChroQueTas: 5-fluorocytosine(1/NA). Source: amr_out/SRR30781135.ChroQueTas/SRR30781135.contigs.ChroQueTaS.Fcy1.1.tsv:9 |
| SRR30781188 | 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/SRR30781188.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR30781188.contigs |
| SRR30781189 | 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/SRR30781189.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR30781189.contigs |
| SRR35650155 | 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/SRR35650155.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR35650155.contigs |
| SRR35650156 | 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/SRR35650156.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR35650156.contigs |
| SRR35650157 | 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/SRR35650157.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR35650157.contigs |
| SRR38394166 | Candida parapsilosis | azole | fluconazole/other azoles | Cyp51 | Y132F | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 Y132F (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(1/NA),Isavuconazole(NA/-1),Posaconazole(NA/-1),Voriconazole(1/-8). Source: amr_out/SRR38394166.ChroQueTas/SRR38394166.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| SRR38394168 | Candida parapsilosis | azole | fluconazole/other azoles | Cyp51 | Y132F | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 Y132F (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(1/NA),Isavuconazole(NA/-1),Posaconazole(NA/-1),Voriconazole(1/-8). Source: amr_out/SRR38394168.ChroQueTas/SRR38394168.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| SRR38394169 | Candida parapsilosis | azole | fluconazole/other azoles | Cyp51 | Y132F | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 Y132F (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(1/NA),Isavuconazole(NA/-1),Posaconazole(NA/-1),Voriconazole(1/-8). Source: amr_out/SRR38394169.ChroQueTas/SRR38394169.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| SRR38394173 | Candida parapsilosis | azole | fluconazole/other azoles | Cyp51 | Y132F | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 Y132F (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(1/NA),Isavuconazole(NA/-1),Posaconazole(NA/-1),Voriconazole(1/-8). Source: amr_out/SRR38394173.ChroQueTas/SRR38394173.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| SRR38394176 | Candida parapsilosis | azole | fluconazole/other azoles | Cyp51 | Y132F | FungAMR MUTATION | FungAMR curated marker detected by ChroQueTas | Curated ChroQueTas/FungAMR marker detected: Cyp51 Y132F (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(1/NA),Isavuconazole(NA/-1),Posaconazole(NA/-1),Voriconazole(1/-8). Source: amr_out/SRR38394176.ChroQueTas/SRR38394176.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| SRR38566159 | 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/SRR38566159.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR38566159.contigs |
| SRR38566164 | 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/SRR38566164.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR38566164.contigs |
| SRR38566207 | 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/SRR38566207.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR38566207.contigs |
| SRR38566258 | 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/SRR38566258.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR38566258.contigs |
| SRR38566259 | 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/SRR38566259.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR38566259.contigs |
| SRR38566263 | 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/SRR38566263.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR38566263.contigs |
| SRR38842632 | 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/SRR38842632.ChroQueTas/SRR38842632.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| SRR38842634 | 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/SRR38842634.ChroQueTas/SRR38842634.contigs.ChroQueTaS.Cyp51.1.tsv:125 |
| SRR38887223 | 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/SRR38887223.ChroQueTas/SRR38887223.contigs.ChroQueTaS.Cyp51.1.tsv:132 |
| SRR38906258 | 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/SRR38906258.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR38906258.contigs |
| SRR38906262 | 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/SRR38906262.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR38906262.contigs |
| SRR38906266 | 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/SRR38906266.ChroQueTas/SRR38906266.contigs.ChroQueTaS.Cyp51.1.tsv:125 |
| SRR38908327 | 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/SRR38908327.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR38908327.contigs |
| SRR38908328 | 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/SRR38908328.ChroQueTas/SRR38908328.contigs.ChroQueTaS.Cyp51.1.tsv:125 |
| SRR38908329 | 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/SRR38908329.ChroQueTas/SRR38908329.contigs.ChroQueTaS.Cyp51.1.tsv:125 |
| SRR38908333 | 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/SRR38908333.ChroQueTas/SRR38908333.contigs.ChroQueTaS.Cyp51.1.tsv:143 |
| SRR38908336 | 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/SRR38908336.ChroQueTas/SRR38908336.contigs.ChroQueTaS.Cyp51.1.tsv:143 |
| SRR38908337 | 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/SRR38908337.ChroQueTas/SRR38908337.contigs.ChroQueTaS.Cyp51.1.tsv:143 |
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 | 5 | 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. |
| Candida tropicalis | PASS | 5 | snippy_core_rc170_tb_style | NA | 29220 | 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. |
| Candidozyma auris | PASS | 12 | snippy_core_rc170_tb_style | NA | 198767 | 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_SUCCESSFUL_CONSENSUS | 0 | diploid_aware_bcftools_iupac_consensus | 2 | NA | Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR23951614:variant_calling_failed,SRR24123449:variant_calling_failed,SRR24123452:variant_calling_failed,SRR24123455:variant_calling_failed,SRR24123459:variant_calling_failed,SRR24123461:variant_calling_failed,SRR24123463:variant_calling_failed,SRR30781078:variant_calling_failed,SRR30781089:variant_calling_failed,SRR30781120:variant_calling_failed,SRR30781135:variant_calling_failed,SRR30781188:variant_calling_failed,SRR30781189:variant_calling_failed |
| Nakaseomyces glabratus | FAILED_CORE_SNP_ALIGNMENT | 8 | haploid_bcftools_consensus | 1 | NA | Consensus FASTA lengths differ after reference-based consensus generation. |
| Pichia kudriavzevii | SKIPPED_TOO_FEW_SUCCESSFUL_CONSENSUS | 0 | diploid_aware_bcftools_iupac_consensus | 2 | NA | Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR38566159:variant_calling_failed,SRR38566164:variant_calling_failed,SRR38566207:variant_calling_failed,SRR38566258:variant_calling_failed,SRR38566259:variant_calling_failed,SRR38566263:variant_calling_failed |
Candida tropicalis
Candidozyma auris
Species without a displayed tree:
- Candida parapsilosis: SKIPPED_SPECIES_NOT_IN_REFERENCE_MANIFEST; samples after species-specific consensus/eligibility = 5; 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.
- Clavispora lusitaniae: SKIPPED_TOO_FEW_SUCCESSFUL_CONSENSUS; samples after species-specific consensus/eligibility = 0; branch = diploid_aware_bcftools_iupac_consensus; note = Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR23951614:variant_calling_failed,SRR24123449:variant_calling_failed,SRR24123452:variant_calling_failed,SRR24123455:variant_calling_failed,SRR24123459:variant_calling_failed,SRR24123461:variant_calling_failed,SRR24123463:variant_calling_failed,SRR30781078:variant_calling_failed,SRR30781089:variant_calling_failed,SRR30781120:variant_calling_failed,SRR30781135:variant_calling_failed,SRR30781188:variant_calling_failed,SRR30781189:variant_calling_failed
- Nakaseomyces glabratus: FAILED_CORE_SNP_ALIGNMENT; samples after species-specific consensus/eligibility = 8; branch = haploid_bcftools_consensus; note = Consensus FASTA lengths differ after reference-based consensus generation.
- Pichia kudriavzevii: SKIPPED_TOO_FEW_SUCCESSFUL_CONSENSUS; samples after species-specific consensus/eligibility = 0; branch = diploid_aware_bcftools_iupac_consensus; note = Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR38566159:variant_calling_failed,SRR38566164:variant_calling_failed,SRR38566207:variant_calling_failed,SRR38566258:variant_calling_failed,SRR38566259:variant_calling_failed,SRR38566263:variant_calling_failed
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 tropicalis | SRR10967519 | SRR35650155 | 1919 | Distinct / review with metadata |
| Candida tropicalis | SRR12823762 | SRR35650157 | 25541 | Distinct / review with metadata |
| Candida tropicalis | SRR35650155 | SRR10967519 | 1919 | Distinct / review with metadata |
| Candida tropicalis | SRR35650156 | SRR35650157 | 2947 | Distinct / review with metadata |
| Candida tropicalis | SRR35650157 | SRR35650155 | 2390 | Distinct / review with metadata |
| Candidozyma auris | SRR38842632 | SRR38887223 | 168 | Distinct / review with metadata |
| Candidozyma auris | SRR38842634 | SRR38908328 | 150 | Distinct / review with metadata |
| Candidozyma auris | SRR38887223 | SRR38842632 | 168 | Distinct / review with metadata |
| Candidozyma auris | SRR38906258 | SRR38906262 | 173 | Distinct / review with metadata |
| Candidozyma auris | SRR38906262 | SRR38906258 | 173 | Distinct / review with metadata |
| Candidozyma auris | SRR38906266 | SRR38908328 | 96 | Distinct / review with metadata |
| Candidozyma auris | SRR38908327 | SRR38906258 | 295 | Distinct / review with metadata |
| Candidozyma auris | SRR38908328 | SRR38906266 | 96 | Distinct / review with metadata |
| Candidozyma auris | SRR38908329 | SRR38908328 | 112 | Distinct / review with metadata |
| Candidozyma auris | SRR38908333 | SRR38908337 | 268 | Distinct / review with metadata |
| Candidozyma auris | SRR38908336 | SRR38908337 | 127 | Distinct / review with metadata |
| Candidozyma auris | SRR38908337 | SRR38908336 | 127 | Distinct / review with metadata |
Pairwise SNP-distance matrix/table
| species | Sample A | Sample B | SNP distance | Compared core-SNP sites |
|---|---|---|---|---|
| Candida tropicalis | SRR10967519 | SRR12823762 | 25648 | 29220 |
| Candida tropicalis | SRR10967519 | SRR35650155 | 1919 | 29220 |
| Candida tropicalis | SRR10967519 | SRR35650156 | 3244 | 29220 |
| Candida tropicalis | SRR10967519 | SRR35650157 | 2675 | 29220 |
| Candida tropicalis | SRR12823762 | SRR35650155 | 25560 | 29220 |
| Candida tropicalis | SRR12823762 | SRR35650156 | 25894 | 29220 |
| Candida tropicalis | SRR12823762 | SRR35650157 | 25541 | 29220 |
| Candida tropicalis | SRR35650155 | SRR35650156 | 3150 | 29220 |
| Candida tropicalis | SRR35650155 | SRR35650157 | 2390 | 29220 |
| Candida tropicalis | SRR35650156 | SRR35650157 | 2947 | 29220 |
| Candidozyma auris | SRR38842632 | SRR38842634 | 40002 | 198767 |
| Candidozyma auris | SRR38842632 | SRR38887223 | 168 | 198767 |
| Candidozyma auris | SRR38842632 | SRR38906258 | 154539 | 198767 |
| Candidozyma auris | SRR38842632 | SRR38906262 | 154590 | 198767 |
| Candidozyma auris | SRR38842632 | SRR38906266 | 39994 | 198767 |
| Candidozyma auris | SRR38842632 | SRR38908327 | 154440 | 198767 |
| Candidozyma auris | SRR38842632 | SRR38908328 | 39981 | 198767 |
| Candidozyma auris | SRR38842632 | SRR38908329 | 39964 | 198767 |
| Candidozyma auris | SRR38842632 | SRR38908333 | 330 | 198767 |
| Candidozyma auris | SRR38842632 | SRR38908336 | 305 | 198767 |
| Candidozyma auris | SRR38842632 | SRR38908337 | 318 | 198767 |
| Candidozyma auris | SRR38842634 | SRR38887223 | 39970 | 198767 |
| Candidozyma auris | SRR38842634 | SRR38906258 | 154785 | 198767 |
| Candidozyma auris | SRR38842634 | SRR38906262 | 154827 | 198767 |
| Candidozyma auris | SRR38842634 | SRR38906266 | 152 | 198767 |
| Candidozyma auris | SRR38842634 | SRR38908327 | 154691 | 198767 |
| Candidozyma auris | SRR38842634 | SRR38908328 | 150 | 198767 |
| Candidozyma auris | SRR38842634 | SRR38908329 | 156 | 198767 |
| Candidozyma auris | SRR38842634 | SRR38908333 | 39997 | 198767 |
| Candidozyma auris | SRR38842634 | SRR38908336 | 40005 | 198767 |
| Candidozyma auris | SRR38842634 | SRR38908337 | 40020 | 198767 |
| Candidozyma auris | SRR38887223 | SRR38906258 | 154514 | 198767 |
| Candidozyma auris | SRR38887223 | SRR38906262 | 154559 | 198767 |
| Candidozyma auris | SRR38887223 | SRR38906266 | 39960 | 198767 |
| Candidozyma auris | SRR38887223 | SRR38908327 | 154415 | 198767 |
| Candidozyma auris | SRR38887223 | SRR38908328 | 39941 | 198767 |
| Candidozyma auris | SRR38887223 | SRR38908329 | 39914 | 198767 |
| Candidozyma auris | SRR38887223 | SRR38908333 | 288 | 198767 |
| Candidozyma auris | SRR38887223 | SRR38908336 | 261 | 198767 |
| Candidozyma auris | SRR38887223 | SRR38908337 | 270 | 198767 |
| Candidozyma auris | SRR38906258 | SRR38906262 | 173 | 198767 |
| Candidozyma auris | SRR38906258 | SRR38906266 | 154781 | 198767 |
| Candidozyma auris | SRR38906258 | SRR38908327 | 295 | 198767 |
| Candidozyma auris | SRR38906258 | SRR38908328 | 154778 | 198767 |
| Candidozyma auris | SRR38906258 | SRR38908329 | 154759 | 198767 |
| Candidozyma auris | SRR38906258 | SRR38908333 | 154537 | 198767 |
| Candidozyma auris | SRR38906258 | SRR38908336 | 154530 | 198767 |
| Candidozyma auris | SRR38906258 | SRR38908337 | 154559 | 198767 |
| Candidozyma auris | SRR38906262 | SRR38906266 | 154829 | 198767 |
| Candidozyma auris | SRR38906262 | SRR38908327 | 314 | 198767 |
| Candidozyma auris | SRR38906262 | SRR38908328 | 154820 | 198767 |
| Candidozyma auris | SRR38906262 | SRR38908329 | 154801 | 198767 |
| Candidozyma auris | SRR38906262 | SRR38908333 | 154574 | 198767 |
| Candidozyma auris | SRR38906262 | SRR38908336 | 154575 | 198767 |
| Candidozyma auris | SRR38906262 | SRR38908337 | 154604 | 198767 |
| Candidozyma auris | SRR38906266 | SRR38908327 | 154695 | 198767 |
| Candidozyma auris | SRR38906266 | SRR38908328 | 96 | 198767 |
| Candidozyma auris | SRR38906266 | SRR38908329 | 116 | 198767 |
| Candidozyma auris | SRR38906266 | SRR38908333 | 39991 | 198767 |
| Candidozyma auris | SRR38906266 | SRR38908336 | 40003 | 198767 |
| Candidozyma auris | SRR38906266 | SRR38908337 | 40018 | 198767 |
| Candidozyma auris | SRR38908327 | SRR38908328 | 154688 | 198767 |
| Candidozyma auris | SRR38908327 | SRR38908329 | 154669 | 198767 |
| Candidozyma auris | SRR38908327 | SRR38908333 | 154440 | 198767 |
| Candidozyma auris | SRR38908327 | SRR38908336 | 154431 | 198767 |
| Candidozyma auris | SRR38908327 | SRR38908337 | 154460 | 198767 |
| Candidozyma auris | SRR38908328 | SRR38908329 | 112 | 198767 |
| Candidozyma auris | SRR38908328 | SRR38908333 | 39968 | 198767 |
| Candidozyma auris | SRR38908328 | SRR38908336 | 39976 | 198767 |
| Candidozyma auris | SRR38908328 | SRR38908337 | 39977 | 198767 |
| Candidozyma auris | SRR38908329 | SRR38908333 | 39947 | 198767 |
| Candidozyma auris | SRR38908329 | SRR38908336 | 39955 | 198767 |
| Candidozyma auris | SRR38908329 | SRR38908337 | 39978 | 198767 |
| Candidozyma auris | SRR38908333 | SRR38908336 | 273 | 198767 |
| Candidozyma auris | SRR38908333 | SRR38908337 | 268 | 198767 |
| Candidozyma auris | SRR38908336 | SRR38908337 | 127 | 198767 |
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.