rMAP-Myc-Candida surveillance report

Integrated Candida fungal genomics report

This report summarizes paired-end fungal genome analysis for Candida-focused surveillance, combining read QC, Kraken2/Bracken species typing, MEGAHIT assembly, QUAST-only assembly contiguity assessment, and genomic antifungal-resistance screening.

Run generated: 2026-05-30 09:39:30 UTCRun stamp: 20260530_093930_UTCCustom Candida Kraken2/Bracken DBMEGAHIT assembly
Samples analyzed34
Top species groups6
Total AMR hits24
Median N5035,946

1. Executive summary

The primary detected fungal species group was Candida albicans. The sample-level cards below provide a compact interpretation of species assignment, QUAST assembly-contiguity metrics, phylogeny status, and genomic AMR screening status.

Interpretation note: genomic antifungal-resistance findings should be treated as screening evidence. Clinically important results should be interpreted with isolate metadata, species identity, validated mutation catalogues, and phenotypic antifungal susceptibility testing where required.

Species distribution

Candida albicans
24
Candida tropicalis
4
Pichia kudriavzevii
3
Nakaseomyces glabratus
1
Clavispora lusitaniae
1
Candida parapsilosis
1

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.

SampleCollection datesitespeciesSpecies confidenceAssembly QCQUAST contiguity QCAMR screenPhylogenySurveillance statusReason / note
SRR30894123NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR30894124NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR30894125NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR30894126NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR30894127NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR30894128NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR30894129NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR30894130NANAPichia kudriavzeviiHighPassPassNo curated marker detectedExcludedReady for surveillance interpretationNo major automated warning flags using species typing, QUAST assembly QC, AMR screening, and phylogeny status
SRR30894131NANANakaseomyces glabratusHighPassPass1 marker(s)ExcludedReviewAMR marker detected
SRR30894132NANACandida albicansHighReviewReviewNo curated marker detectedIncluded / eligibleReviewQUAST assembly QC
SRR30894133NANACandida albicansModerateReviewReview1 marker(s)Included / eligibleReviewspecies confidence; QUAST assembly QC; AMR marker detected
SRR30894134NANAPichia kudriavzeviiModerateReviewReviewNo curated marker detectedExcludedReviewspecies confidence; QUAST assembly QC
SRR30894135NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR30894136NANACandida tropicalisHighReviewReviewNo curated marker detectedIncluded / eligibleReviewQUAST assembly QC
SRR30894137NANAPichia kudriavzeviiLow / reviewReviewReviewNo curated marker detectedExcludedReviewspecies confidence; QUAST assembly QC
SRR30894138NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR30894139NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR30894140NANAClavispora lusitaniaeHighPassPassNo curated marker detectedExcludedReady for surveillance interpretationNo major automated warning flags using species typing, QUAST assembly QC, AMR screening, and phylogeny status
SRR30894141NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR30894142NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR30894143NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR30894144NANACandida tropicalisHighReviewReviewNo curated marker detectedIncluded / eligibleReviewQUAST assembly QC
SRR30894145NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR30894146NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR30894147NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR33417537NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR33417538NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR33417539NANACandida parapsilosisHighPassPassNo curated marker detectedExcludedReady for surveillance interpretationNo major automated warning flags using species typing, QUAST assembly QC, AMR screening, and phylogeny status
SRR33417540NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR33417541NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR33417542NANACandida tropicalisHighReviewReviewNo curated marker detectedIncluded / eligibleReviewQUAST assembly QC
SRR33417543NANACandida tropicalisHighReviewReviewNo curated marker detectedIncluded / eligibleReviewQUAST assembly QC
SRR33417544NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR33417545NANACandida albicansHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected

3. Surveillance metadata

No surveillance metadata TSV was provided. Add rMAP_Candida.surveillance_metadata_tsv to your input JSON to display collection date, country/site, specimen type, patient group, facility/ward, and sequencing platform.

4. Sample-level surveillance summary

SRR30894123

Candida albicans Review
Species reads99.21%
Contigs1,506
N5033,842
GC (%)33.42

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR30894124

Candida albicans Review
Species reads99.54%
Contigs1,237
N5052,568
GC (%)33.43

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR30894125

Candida albicans Review
Species reads99.29%
Contigs1,652
N5024,041
GC (%)33.40

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR30894126

Candida albicans Review
Species reads99.34%
Contigs1,552
N5029,071
GC (%)33.41

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR30894127

Candida albicans Review
Species reads99.49%
Contigs1,623
N5034,114
GC (%)33.42

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR30894128

Candida albicans Review
Species reads99.36%
Contigs1,603
N5042,869
GC (%)33.42

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR30894129

Candida albicans Review
Species reads99.55%
Contigs1,329
N5040,138
GC (%)33.39

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR30894130

Pichia kudriavzevii Ready for surveillance interpretation
Species reads97.84%
Contigs699
N5037,093
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: SRR30894130:variant_calling_failed,SRR30894134:variant_calling_failed,SRR30894137:variant_calling_failed

SRR30894131

Nakaseomyces glabratus Review
Species reads99.84%
Contigs830
N5035,217
GC (%)38.52

1 AMR hit(s) Species confidence: High Phylogeny: Excluded

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Requires at least 3 samples for a species-specific tree.

SRR30894132

Candida albicans Review
Species reads99.49%
Contigs9,126
N501,253
GC (%)33.35

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 (24 samples)

SRR30894133

Candida albicans Review
Species reads89.93%
Contigs3,328
N5021,164
GC (%)33.55

1 AMR hit(s) Species confidence: Moderate Phylogeny: Included / eligible

Interpretation: species confidence; QUAST assembly QC; AMR marker detected. Species note: Top species abundance 80–95%; review for possible mixed signal. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR30894134

Pichia kudriavzevii Review
Species reads83.79%
Contigs2,922
N5012,632
GC (%)37.88

No curated genomic AMR marker detected — not susceptible Species confidence: Moderate Phylogeny: Excluded

Interpretation: species confidence; QUAST assembly QC. Species note: Top species abundance 80–95%; review for possible mixed signal. Phylogeny note: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR30894130:variant_calling_failed,SRR30894134:variant_calling_failed,SRR30894137:variant_calling_failed

SRR30894135

Candida albicans Review
Species reads99.09%
Contigs1,382
N5037,919
GC (%)33.39

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR30894136

Candida tropicalis Review
Species reads99.96%
Contigs1,506
N5019,835
GC (%)32.93

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 (4 samples)

SRR30894137

Pichia kudriavzevii Review
Species reads74.68%
Contigs6,237
N507,654
GC (%)35.55

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: Fewer than the minimum number of samples produced consensus FASTA files. Failed: SRR30894130:variant_calling_failed,SRR30894134:variant_calling_failed,SRR30894137:variant_calling_failed

SRR30894138

Candida albicans Review
Species reads99.38%
Contigs1,901
N5027,035
GC (%)33.48

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 (24 samples)

SRR30894139

Candida albicans Review
Species reads98.56%
Contigs1,586
N5040,477
GC (%)33.41

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR30894140

Clavispora lusitaniae Ready for surveillance interpretation
Species reads95.10%
Contigs1,063
N50111,646
GC (%)44.03

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.

SRR30894141

Candida albicans Review
Species reads97.47%
Contigs1,923
N5020,207
GC (%)33.41

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR30894142

Candida albicans Review
Species reads99.27%
Contigs1,648
N5024,044
GC (%)33.42

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR30894143

Candida albicans Review
Species reads99.31%
Contigs1,438
N5036,675
GC (%)33.40

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR30894144

Candida tropicalis Review
Species reads99.01%
Contigs9,505
N503,788
GC (%)33.26

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 (4 samples)

SRR30894145

Candida albicans Review
Species reads99.45%
Contigs1,734
N5032,664
GC (%)33.74

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 (24 samples)

SRR30894146

Candida albicans Review
Species reads99.34%
Contigs1,308
N5037,168
GC (%)33.41

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR30894147

Candida albicans Review
Species reads99.36%
Contigs1,138
N5052,837
GC (%)33.44

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 (24 samples)

SRR33417537

Candida albicans Review
Species reads99.37%
Contigs1,354
N5052,873
GC (%)33.40

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR33417538

Candida albicans Review
Species reads99.52%
Contigs1,143
N5058,607
GC (%)33.37

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR33417539

Candida parapsilosis Ready for surveillance interpretation
Species reads100.00%
Contigs366
N50118,140
GC (%)38.65

No curated genomic AMR marker detected — not susceptible Species confidence: High Phylogeny: Excluded

Interpretation: No major automated warning flags using species typing, QUAST assembly QC, AMR screening, and phylogeny status. Species note: Top species abundance ≥95%. Phylogeny note: Skipped by rc172 phylogeny guard because this detected species is not among the defined Candida species with an exported reference FASTA. Valid species with references are still processed.

SRR33417540

Candida albicans Review
Species reads99.41%
Contigs1,270
N5052,398
GC (%)33.40

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR33417541

Candida albicans Review
Species reads99.33%
Contigs1,143
N5060,507
GC (%)33.41

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR33417542

Candida tropicalis Review
Species reads99.84%
Contigs6,414
N507,269
GC (%)33.23

No curated genomic AMR marker detected — not susceptible Species confidence: High Phylogeny: Included / eligible

Interpretation: QUAST assembly QC. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (4 samples)

SRR33417543

Candida tropicalis Review
Species reads99.83%
Contigs6,401
N507,197
GC (%)33.22

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 (4 samples)

SRR33417544

Candida albicans Review
Species reads99.35%
Contigs1,270
N5058,226
GC (%)33.42

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 samples)

SRR33417545

Candida albicans Review
Species reads99.32%
Contigs1,598
N5048,557
GC (%)33.43

1 AMR hit(s) Species confidence: High Phylogeny: Included / eligible

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Species group passed phylogeny stage (24 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.

SampleTop speciesReads (%)clade_readstaxon_readstaxidevidence
SRR30894123Candida albicans
99.21%		1,047,3521,047,3525476Bracken species-level abundance
SRR30894124Candida albicans
99.54%		4,937,4084,937,4085476Bracken species-level abundance
SRR30894125Candida albicans
99.29%		758,251758,2515476Bracken species-level abundance
SRR30894126Candida albicans
99.34%		881,807881,8075476Bracken species-level abundance
SRR30894127Candida albicans
99.49%		1,126,7591,126,7595476Bracken species-level abundance
SRR30894128Candida albicans
99.36%		1,385,3391,385,3395476Bracken species-level abundance
SRR30894129Candida albicans
99.55%		1,291,3921,291,3925476Bracken species-level abundance
SRR30894130Pichia kudriavzevii
97.84%		805,230805,2304909Bracken species-level abundance
SRR30894131Nakaseomyces glabratus
99.84%		706,009706,0095478Bracken species-level abundance
SRR30894132Candida albicans
99.49%		241,553241,5535476Bracken species-level abundance
SRR30894133Candida albicans
89.93%		743,615743,6155476Bracken species-level abundance
SRR30894134Pichia kudriavzevii
83.79%		470,181470,1814909Bracken species-level abundance
SRR30894135Candida albicans
99.09%		1,294,4421,294,4425476Bracken species-level abundance
SRR30894136Candida tropicalis
99.96%		881,766881,7665482Bracken species-level abundance
SRR30894137Pichia kudriavzevii
74.68%		971,564971,5644909Bracken species-level abundance
SRR30894138Candida albicans
99.38%		1,132,2941,132,2945476Bracken species-level abundance
SRR30894139Candida albicans
98.56%		1,898,1691,898,1695476Bracken species-level abundance
SRR30894140Clavispora lusitaniae
95.10%		1,124,5721,124,57236911Bracken species-level abundance
SRR30894141Candida albicans
97.47%		631,452631,4525476Bracken species-level abundance
SRR30894142Candida albicans
99.27%		758,550758,5505476Bracken species-level abundance
SRR30894143Candida albicans
99.31%		1,414,3631,414,3635476Bracken species-level abundance
SRR30894144Candida tropicalis
99.01%		993,271993,2715482Bracken species-level abundance
SRR30894145Candida albicans
99.45%		922,061922,0615476Bracken species-level abundance
SRR30894146Candida albicans
99.34%		1,225,9231,225,9235476Bracken species-level abundance
SRR30894147Candida albicans
99.36%		2,969,3552,969,3555476Bracken species-level abundance
SRR33417537Candida albicans
99.37%		6,006,7666,006,7665476Bracken species-level abundance
SRR33417538Candida albicans
99.52%		5,076,2195,076,2195476Bracken species-level abundance
SRR33417539Candida parapsilosis
100.00%		5,428,0525,428,0525480Bracken species-level abundance
SRR33417540Candida albicans
99.41%		5,113,1145,113,1145476Bracken species-level abundance
SRR33417541Candida albicans
99.33%		4,986,4984,986,4985476Bracken species-level abundance
SRR33417542Candida tropicalis
99.84%		4,165,8554,165,8555482Bracken species-level abundance
SRR33417543Candida tropicalis
99.83%		3,768,0213,768,0215482Bracken species-level abundance
SRR33417544Candida albicans
99.35%		4,025,7374,025,7375476Bracken species-level abundance
SRR33417545Candida albicans
99.32%		5,233,4185,233,4185476Bracken species-level abundance

6. MEGAHIT assembly summary

SamplecontigsTotal bpN50Largest contig
SRR308941231,50614,718,38433,842182,321
SRR308941241,23714,709,48352,568255,210
SRR308941251,65214,583,20724,041229,712
SRR308941261,55214,659,38329,071158,688
SRR308941271,62314,788,64934,114276,896
SRR308941281,60314,868,93142,869190,964
SRR308941291,32914,686,43440,138188,702
SRR3089413069910,755,45437,093180,358
SRR3089413183012,194,93335,217143,273
SRR308941329,12610,253,5881,25321,477
SRR308941333,32815,830,06021,164170,943
SRR308941342,92211,749,48412,63294,979
SRR308941351,38214,676,40037,919169,037
SRR308941361,50614,502,71319,83590,180
SRR308941376,23724,264,9587,654221,754
SRR308941381,90114,893,01227,035136,200
SRR308941391,58614,895,58640,477238,813
SRR308941401,06312,670,360111,646330,417
SRR308941411,92314,613,18920,207190,535
SRR308941421,64814,530,41024,044190,685
SRR308941431,43814,769,77936,675174,791
SRR308941449,50525,045,4873,788124,105
SRR308941451,73414,875,17032,664160,637
SRR308941461,30814,649,55537,168195,399
SRR308941471,13814,630,58152,837367,586
SRR334175371,35414,797,66352,873275,261
SRR334175381,14314,605,24158,607307,598
SRR3341753936612,897,863118,140473,263
SRR334175401,27014,771,18252,398377,705
SRR334175411,14314,708,26960,507344,955
SRR334175426,41427,931,2087,269135,959
SRR334175436,40127,891,6827,197130,373
SRR334175441,27014,805,11458,226340,509
SRR334175451,59815,010,32548,557271,365

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# contigsLargest contigTotal lengthGC (%)N50
SRR308941231,506182,32114,718,38433.4233,842
SRR308941241,237255,21014,709,48333.4352,568
SRR308941251,652229,71214,583,20733.4024,041
SRR308941261,552158,68814,659,38333.4129,071
SRR308941271,623276,89614,788,64933.4234,114
SRR308941281,603190,96414,868,93133.4242,869
SRR308941291,329188,70214,686,43433.3940,138
SRR30894130699180,35810,755,45438.2737,093
SRR30894131830143,27312,194,93338.5235,217
SRR308941329,12621,47710,253,58833.351,253
SRR308941333,328170,94315,830,06033.5521,164
SRR308941342,92294,97911,749,48437.8812,632
SRR308941351,382169,03714,676,40033.3937,919
SRR308941361,50690,18014,502,71332.9319,835
SRR308941376,237221,75424,264,95835.557,654
SRR308941381,901136,20014,893,01233.4827,035
SRR308941391,586238,81314,895,58633.4140,477
SRR308941401,063330,41712,670,36044.03111,646
SRR308941411,923190,53514,613,18933.4120,207
SRR308941421,648190,68514,530,41033.4224,044
SRR308941431,438174,79114,769,77933.4036,675
SRR308941449,505124,10525,045,48733.263,788
SRR308941451,734160,63714,875,17033.7432,664
SRR308941461,308195,39914,649,55533.4137,168
SRR308941471,138367,58614,630,58133.4452,837
SRR334175371,354275,26114,797,66333.4052,873
SRR334175381,143307,59814,605,24133.3758,607
SRR33417539366473,26312,897,86338.65118,140
SRR334175401,270377,70514,771,18233.4052,398
SRR334175411,143344,95514,708,26933.4160,507
SRR334175426,414135,95927,931,20833.237,269
SRR334175436,401130,37327,891,68233.227,197
SRR334175441,270340,50914,805,11433.4258,226
SRR334175451,598271,36515,010,32533.4348,557

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.

Samplespeciesdrug_classdrugGene / statusmutationeffectevidence_levelinterpretation
SRR30894123Candida albicansazolefluconazole/other azolesCyp51E266DFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Cyp51 E266D (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-1). Source: amr_out/SRR30894123.ChroQueTas/SRR30894123.contigs.ChroQueTaS.Cyp51.1.tsv:266
SRR30894124Candida albicansazolefluconazole/other azolesMrr1E1020QFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Mrr1 E1020Q (FungAMR MUTATION). Drug evidence from ChroQueTas: Brefeldin_A(NA/-1),Cerulenin(NA/-1),Fluconazole(NA/-1). Source: amr_out/SRR30894124.ChroQueTas/SRR30894124.contigs.ChroQueTaS.Mrr1.1.tsv:1020
SRR30894125Candida albicansazolefluconazole/other azolesMrr1E1020QFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Mrr1 E1020Q (FungAMR MUTATION). Drug evidence from ChroQueTas: Brefeldin_A(NA/-1),Cerulenin(NA/-1),Fluconazole(NA/-1). Source: amr_out/SRR30894125.ChroQueTas/SRR30894125.contigs.ChroQueTaS.Mrr1.1.tsv:1020
SRR30894126Candida albicansazolefluconazole/other azolesCyp51E266DFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Cyp51 E266D (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-1). Source: amr_out/SRR30894126.ChroQueTas/SRR30894126.contigs.ChroQueTaS.Cyp51.1.tsv:266
SRR30894127Candida albicansazolefluconazole/other azolesMrr1E1020QFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Mrr1 E1020Q (FungAMR MUTATION). Drug evidence from ChroQueTas: Brefeldin_A(NA/-1),Cerulenin(NA/-1),Fluconazole(NA/-1). Source: amr_out/SRR30894127.ChroQueTas/SRR30894127.contigs.ChroQueTaS.Mrr1.1.tsv:1020
SRR30894128Candida albicansazolefluconazole/other azolesMrr1E1020QFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Mrr1 E1020Q (FungAMR MUTATION). Drug evidence from ChroQueTas: Brefeldin_A(NA/-1),Cerulenin(NA/-1),Fluconazole(NA/-1). Source: amr_out/SRR30894128.ChroQueTas/SRR30894128.contigs.ChroQueTaS.Mrr1.1.tsv:1020
SRR30894129Candida albicansazolefluconazole/other azolesCyp51D116EFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated 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/SRR30894129.ChroQueTas/SRR30894129.contigs.ChroQueTaS.Cyp51.1.tsv:116
SRR30894130Pichia kudriavzeviiazole/otherfluconazole/otherNo marker — not susceptibleNANAscanner_detected_candidate_markerThe 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/SRR30894130.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR30894130.contigs
SRR30894131Nakaseomyces glabratusantifungalspecies-aware antifungal panelBen1V254IFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Ben1 V254I (FungAMR MUTATION). Drug evidence from ChroQueTas: Various(NA/-8). Source: amr_out/SRR30894131.ChroQueTas/SRR30894131.contigs.ChroQueTaS.Ben1.1.tsv:254
SRR30894132Candida albicansazole/otherfluconazole/otherNo marker — not susceptibleNANAscanner_detected_candidate_markerThe 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/SRR30894132.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR30894132.contigs
SRR30894133Candida albicansazolefluconazole/other azolesMrr1E1020QFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Mrr1 E1020Q (FungAMR MUTATION). Drug evidence from ChroQueTas: Brefeldin_A(NA/-1),Cerulenin(NA/-1),Fluconazole(NA/-1). Source: amr_out/SRR30894133.ChroQueTas/SRR30894133.contigs.ChroQueTaS.Mrr1.1.tsv:1020
SRR30894134Pichia kudriavzeviiazole/otherfluconazole/otherNo marker — not susceptibleNANAscanner_detected_candidate_markerThe 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/SRR30894134.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR30894134.contigs
SRR30894135Candida albicansazolefluconazole/other azolesCap1M140IFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Cap1 M140I (FungAMR MUTATION). Drug evidence from ChroQueTas: Clotrimazole(3/NA),Fluconazole(3/NA),Fluconazole(NA/-1),Isavuconazole(3/NA),Itraconazole(3/NA),Itraconazole(NA/-1),Ketoconazole(NA/-1),Posaconazole(3/NA),Posaconazole(NA/-1),Voriconazole(3/NA),Voriconazole(NA/-1). Source: amr_out/SRR30894135.ChroQueTas/SRR30894135.contigs.ChroQueTaS.Cap1.1.tsv:140
SRR30894136Candida tropicalisazole/otherfluconazole/otherNo marker — not susceptibleNANAscanner_detected_candidate_markerThe 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/SRR30894136.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR30894136.contigs
SRR30894137Pichia kudriavzeviiazole/otherfluconazole/otherNo marker — not susceptibleNANAscanner_detected_candidate_markerThe 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/SRR30894137.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR30894137.contigs
SRR30894138Candida albicansazolefluconazole/other azolesCyp51E266DFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Cyp51 E266D (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-1). Source: amr_out/SRR30894138.ChroQueTas/SRR30894138.contigs.ChroQueTaS.Cyp51.1.tsv:266
SRR30894139Candida albicansazolefluconazole/other azolesCyp51E266DFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Cyp51 E266D (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-1). Source: amr_out/SRR30894139.ChroQueTas/SRR30894139.contigs.ChroQueTaS.Cyp51.1.tsv:266
SRR30894140Clavispora lusitaniaeazole/otherfluconazole/otherNo marker — not susceptibleNANAscanner_detected_candidate_markerThe 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/SRR30894140.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR30894140.contigs
SRR30894141Candida albicansazolefluconazole/other azolesMrr1E1020QFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Mrr1 E1020Q (FungAMR MUTATION). Drug evidence from ChroQueTas: Brefeldin_A(NA/-1),Cerulenin(NA/-1),Fluconazole(NA/-1). Source: amr_out/SRR30894141.ChroQueTas/SRR30894141.contigs.ChroQueTaS.Mrr1.1.tsv:1020
SRR30894142Candida albicansazolefluconazole/other azolesMrr1E1020QFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Mrr1 E1020Q (FungAMR MUTATION). Drug evidence from ChroQueTas: Brefeldin_A(NA/-1),Cerulenin(NA/-1),Fluconazole(NA/-1). Source: amr_out/SRR30894142.ChroQueTas/SRR30894142.contigs.ChroQueTaS.Mrr1.1.tsv:1020
SRR30894143Candida albicansazolefluconazole/other azolesCyp51E266DFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Cyp51 E266D (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-1). Source: amr_out/SRR30894143.ChroQueTas/SRR30894143.contigs.ChroQueTaS.Cyp51.1.tsv:266
SRR30894144Candida tropicalisazole/otherfluconazole/otherNo marker — not susceptibleNANAscanner_detected_candidate_markerThe 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/SRR30894144.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR30894144.contigs
SRR30894145Candida albicansazolefluconazole/other azolesCyp51E266DFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Cyp51 E266D (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-1). Source: amr_out/SRR30894145.ChroQueTas/SRR30894145.contigs.ChroQueTaS.Cyp51.1.tsv:266
SRR30894146Candida albicansazolefluconazole/other azolesCyp51E266DFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Cyp51 E266D (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-1). Source: amr_out/SRR30894146.ChroQueTas/SRR30894146.contigs.ChroQueTaS.Cyp51.1.tsv:266
SRR30894147Candida albicansazolefluconazole/other azolesCyp51E266DFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Cyp51 E266D (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-1). Source: amr_out/SRR30894147.ChroQueTas/SRR30894147.contigs.ChroQueTaS.Cyp51.1.tsv:266
SRR33417537Candida albicansazolefluconazole/other azolesCyp51E266DFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Cyp51 E266D (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-1). Source: amr_out/SRR33417537.ChroQueTas/SRR33417537.contigs.ChroQueTaS.Cyp51.1.tsv:266
SRR33417538Candida albicansazolefluconazole/other azolesCyp51V437IFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Cyp51 V437I (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(8/-2),Isavuconazole(8/NA),Itraconazole(8/-8),Posaconazole(8/NA),Voriconazole(8/-8). Source: amr_out/SRR33417538.ChroQueTas/SRR33417538.contigs.ChroQueTaS.Cyp51.1.tsv:437
SRR33417539Candida parapsilosisazole/otherfluconazole/otherNo marker — not susceptibleNANAscanner_detected_candidate_markerThe AMR scanner produced text consistent with a possible curated resistance marker, but rc151 could not parse an exact ChroQueTas marker row. Review fungal_amr.raw.tsv and fungal_amr.log for the exact record: amr_out/SRR33417539.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR33417539.contigs
SRR33417540Candida albicansazolefluconazole/other azolesCyp51E266DFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Cyp51 E266D (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-1). Source: amr_out/SRR33417540.ChroQueTas/SRR33417540.contigs.ChroQueTaS.Cyp51.1.tsv:266
SRR33417541Candida albicansazolefluconazole/other azolesCyp51E266DFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Cyp51 E266D (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-1). Source: amr_out/SRR33417541.ChroQueTas/SRR33417541.contigs.ChroQueTaS.Cyp51.1.tsv:266
SRR33417542Candida tropicalisazole/otherfluconazole/otherNo marker — not susceptibleNANAscanner_detected_candidate_markerThe AMR scanner produced text consistent with a possible curated resistance marker, but rc151 could not parse an exact ChroQueTas marker row. Review fungal_amr.raw.tsv and fungal_amr.log for the exact record: amr_out/SRR33417542.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR33417542.contigs
SRR33417543Candida tropicalisazole/otherfluconazole/otherNo marker — not susceptibleNANAscanner_detected_candidate_markerThe 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/SRR33417543.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR33417543.contigs
SRR33417544Candida albicansazolefluconazole/other azolesCyp51E266DFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Cyp51 E266D (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-1). Source: amr_out/SRR33417544.ChroQueTas/SRR33417544.contigs.ChroQueTaS.Cyp51.1.tsv:266
SRR33417545Candida albicansazolefluconazole/other azolesCyp51D116EFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated 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/SRR33417545.ChroQueTas/SRR33417545.contigs.ChroQueTaS.Cyp51.1.tsv:116

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.

SpeciesStatusSamplesVariant-calling branchPloidy modelCore variable sitesNotes
Candida parapsilosisSKIPPED_SPECIES_NOT_IN_REFERENCE_MANIFEST1NANANASkipped 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 albicansPASS24snippy_core_rc170_tb_styleNA59rc170 used the rMAP-TB-style Snippy -> snippy-core branch. Species grouping was based on Kraken2/Bracken top-species calls; mixed-species trees are intentionally avoided. Recombination is not explicitly filtered.
Candida tropicalisPASS4snippy_core_rc170_tb_styleNA23707rc170 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 lusitaniaeSKIPPED_TOO_FEW_SAMPLES1diploid_aware_bcftools_iupac_consensus2NARequires at least 3 samples for a species-specific tree.
Nakaseomyces glabratusSKIPPED_TOO_FEW_SAMPLES1haploid_bcftools_consensus1NARequires at least 3 samples for a species-specific tree.
Pichia kudriavzeviiSKIPPED_TOO_FEW_SUCCESSFUL_CONSENSUS0diploid_aware_bcftools_iupac_consensus2NAFewer than the minimum number of samples produced consensus FASTA files. Failed: SRR30894130:variant_calling_failed,SRR30894134:variant_calling_failed,SRR30894137:variant_calling_failed

Candida albicans

Candida albicans core-SNP phylogenetic tree

Candida tropicalis

Candida tropicalis core-SNP phylogenetic tree
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.
  • Clavispora lusitaniae: 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.
  • Nakaseomyces glabratus: SKIPPED_TOO_FEW_SAMPLES; samples after species-specific consensus/eligibility = 1; branch = haploid_bcftools_consensus; note = Requires at least 3 samples for a species-specific tree.
  • 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: SRR30894130:variant_calling_failed,SRR30894134:variant_calling_failed,SRR30894137: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

speciesSampleClosest sampleSNP distanceConservative cluster flag
Candida albicansSRR30894123SRR308941460Possible close genetic relationship
Candida albicansSRR30894124SRR308941250Possible close genetic relationship
Candida albicansSRR30894125SRR308941240Possible close genetic relationship
Candida albicansSRR30894126SRR308941231Possible close genetic relationship
Candida albicansSRR30894127SRR308941240Possible close genetic relationship
Candida albicansSRR30894128SRR308941291Possible close genetic relationship
Candida albicansSRR30894129SRR308941380Possible close genetic relationship
Candida albicansSRR30894132SRR308941352Possible close genetic relationship
Candida albicansSRR30894133SRR308941231Possible close genetic relationship
Candida albicansSRR30894135SRR308941322Possible close genetic relationship
Candida albicansSRR30894138SRR308941290Possible close genetic relationship
Candida albicansSRR30894139SRR308941290Possible close genetic relationship
Candida albicansSRR30894141SRR308941240Possible close genetic relationship
Candida albicansSRR30894142SRR308941240Possible close genetic relationship
Candida albicansSRR30894143SRR308941233Possible close genetic relationship
Candida albicansSRR30894145SRR308941231Possible close genetic relationship
Candida albicansSRR30894146SRR308941230Possible close genetic relationship
Candida albicansSRR30894147SRR308941232Possible close genetic relationship
Candida albicansSRR33417537SRR334175440Possible close genetic relationship
Candida albicansSRR33417538SRR308941238Possible close genetic relationship
Candida albicansSRR33417540SRR308941232Possible close genetic relationship
Candida albicansSRR33417541SRR308941231Possible close genetic relationship
Candida albicansSRR33417544SRR334175370Possible close genetic relationship
Candida albicansSRR33417545SRR3089412315Possible close genetic relationship
Candida tropicalisSRR30894136SRR3341754218799Distinct / review with metadata
Candida tropicalisSRR30894144SRR33417542940Distinct / review with metadata
Candida tropicalisSRR33417542SRR3341754315Possible close genetic relationship
Candida tropicalisSRR33417543SRR3341754215Possible close genetic relationship

Pairwise SNP-distance matrix/table

speciesSample ASample BSNP distanceCompared core-SNP sites
Candida albicansSRR30894123SRR30894124159
Candida albicansSRR30894123SRR30894125159
Candida albicansSRR30894123SRR30894126159
Candida albicansSRR30894123SRR30894127159
Candida albicansSRR30894123SRR30894128459
Candida albicansSRR30894123SRR30894129359
Candida albicansSRR30894123SRR30894132959
Candida albicansSRR30894123SRR30894133159
Candida albicansSRR30894123SRR30894135759
Candida albicansSRR30894123SRR30894138359
Candida albicansSRR30894123SRR30894139359
Candida albicansSRR30894123SRR30894141159
Candida albicansSRR30894123SRR30894142159
Candida albicansSRR30894123SRR30894143359
Candida albicansSRR30894123SRR30894145159
Candida albicansSRR30894123SRR30894146059
Candida albicansSRR30894123SRR30894147259
Candida albicansSRR30894123SRR33417537759
Candida albicansSRR30894123SRR33417538859
Candida albicansSRR30894123SRR33417540259
Candida albicansSRR30894123SRR33417541159
Candida albicansSRR30894123SRR33417544759
Candida albicansSRR30894123SRR334175451559
Candida albicansSRR30894124SRR30894125059
Candida albicansSRR30894124SRR30894126259
Candida albicansSRR30894124SRR30894127059
Candida albicansSRR30894124SRR30894128359
Candida albicansSRR30894124SRR30894129259
Candida albicansSRR30894124SRR30894132859
Candida albicansSRR30894124SRR30894133259
Candida albicansSRR30894124SRR30894135659
Candida albicansSRR30894124SRR30894138259
Candida albicansSRR30894124SRR30894139259
Candida albicansSRR30894124SRR30894141059
Candida albicansSRR30894124SRR30894142059
Candida albicansSRR30894124SRR30894143459
Candida albicansSRR30894124SRR30894145259
Candida albicansSRR30894124SRR30894146159
Candida albicansSRR30894124SRR30894147359
Candida albicansSRR30894124SRR33417537659
Candida albicansSRR30894124SRR33417538959
Candida albicansSRR30894124SRR33417540359
Candida albicansSRR30894124SRR33417541259
Candida albicansSRR30894124SRR33417544659
Candida albicansSRR30894124SRR334175451659
Candida albicansSRR30894125SRR30894126259
Candida albicansSRR30894125SRR30894127059
Candida albicansSRR30894125SRR30894128359
Candida albicansSRR30894125SRR30894129259
Candida albicansSRR30894125SRR30894132859
Candida albicansSRR30894125SRR30894133259
Candida albicansSRR30894125SRR30894135659
Candida albicansSRR30894125SRR30894138259
Candida albicansSRR30894125SRR30894139259
Candida albicansSRR30894125SRR30894141059
Candida albicansSRR30894125SRR30894142059
Candida albicansSRR30894125SRR30894143459
Candida albicansSRR30894125SRR30894145259
Candida albicansSRR30894125SRR30894146159
Candida albicansSRR30894125SRR30894147359
Candida albicansSRR30894125SRR33417537659
Candida albicansSRR30894125SRR33417538959
Candida albicansSRR30894125SRR33417540359
Candida albicansSRR30894125SRR33417541259
Candida albicansSRR30894125SRR33417544659
Candida albicansSRR30894125SRR334175451659
Candida albicansSRR30894126SRR30894127259
Candida albicansSRR30894126SRR30894128559
Candida albicansSRR30894126SRR30894129459
Candida albicansSRR30894126SRR308941321059
Candida albicansSRR30894126SRR30894133259
Candida albicansSRR30894126SRR30894135859
Candida albicansSRR30894126SRR30894138459
Candida albicansSRR30894126SRR30894139459
Candida albicansSRR30894126SRR30894141259
Candida albicansSRR30894126SRR30894142259
Candida albicansSRR30894126SRR30894143459
Candida albicansSRR30894126SRR30894145259
Candida albicansSRR30894126SRR30894146159
Candida albicansSRR30894126SRR30894147359
Candida albicansSRR30894126SRR33417537859
Candida albicansSRR30894126SRR33417538959
Candida albicansSRR30894126SRR33417540359
Candida albicansSRR30894126SRR33417541259
Candida albicansSRR30894126SRR33417544859
Candida albicansSRR30894126SRR334175451659
Candida albicansSRR30894127SRR30894128359
Candida albicansSRR30894127SRR30894129259
Candida albicansSRR30894127SRR30894132859
Candida albicansSRR30894127SRR30894133259
Candida albicansSRR30894127SRR30894135659
Candida albicansSRR30894127SRR30894138259
Candida albicansSRR30894127SRR30894139259
Candida albicansSRR30894127SRR30894141059
Candida albicansSRR30894127SRR30894142059
Candida albicansSRR30894127SRR30894143459
Candida albicansSRR30894127SRR30894145259
Candida albicansSRR30894127SRR30894146159
Candida albicansSRR30894127SRR30894147359
Candida albicansSRR30894127SRR33417537659
Candida albicansSRR30894127SRR33417538959
Candida albicansSRR30894127SRR33417540359
Candida albicansSRR30894127SRR33417541259
Candida albicansSRR30894127SRR33417544659
Candida albicansSRR30894127SRR334175451659
Candida albicansSRR30894128SRR30894129159
Candida albicansSRR30894128SRR30894132759
Candida albicansSRR30894128SRR30894133559
Candida albicansSRR30894128SRR30894135559
Candida albicansSRR30894128SRR30894138159
Candida albicansSRR30894128SRR30894139159
Candida albicansSRR30894128SRR30894141359
Candida albicansSRR30894128SRR30894142359
Candida albicansSRR30894128SRR30894143759
Candida albicansSRR30894128SRR30894145559
Candida albicansSRR30894128SRR30894146459
Candida albicansSRR30894128SRR30894147659
Candida albicansSRR30894128SRR33417537559
Candida albicansSRR30894128SRR334175381259
Candida albicansSRR30894128SRR33417540659
Candida albicansSRR30894128SRR33417541559
Candida albicansSRR30894128SRR33417544559
Candida albicansSRR30894128SRR334175451959
Candida albicansSRR30894129SRR30894132659
Candida albicansSRR30894129SRR30894133459
Candida albicansSRR30894129SRR30894135459
Candida albicansSRR30894129SRR30894138059
Candida albicansSRR30894129SRR30894139059
Candida albicansSRR30894129SRR30894141259
Candida albicansSRR30894129SRR30894142259
Candida albicansSRR30894129SRR30894143659
Candida albicansSRR30894129SRR30894145459
Candida albicansSRR30894129SRR30894146359
Candida albicansSRR30894129SRR30894147559
Candida albicansSRR30894129SRR33417537459
Candida albicansSRR30894129SRR334175381159
Candida albicansSRR30894129SRR33417540559
Candida albicansSRR30894129SRR33417541459
Candida albicansSRR30894129SRR33417544459
Candida albicansSRR30894129SRR334175451859
Candida albicansSRR30894132SRR308941331059
Candida albicansSRR30894132SRR30894135259
Candida albicansSRR30894132SRR30894138659
Candida albicansSRR30894132SRR30894139659
Candida albicansSRR30894132SRR30894141859
Candida albicansSRR30894132SRR30894142859
Candida albicansSRR30894132SRR308941431259
Candida albicansSRR30894132SRR308941451059
Candida albicansSRR30894132SRR30894146959
Candida albicansSRR30894132SRR308941471159
Candida albicansSRR30894132SRR334175371059
Candida albicansSRR30894132SRR334175381759
Candida albicansSRR30894132SRR334175401159
Candida albicansSRR30894132SRR334175411059
Candida albicansSRR30894132SRR334175441059
Candida albicansSRR30894132SRR334175452259
Candida albicansSRR30894133SRR30894135859
Candida albicansSRR30894133SRR30894138459
Candida albicansSRR30894133SRR30894139459
Candida albicansSRR30894133SRR30894141259
Candida albicansSRR30894133SRR30894142259
Candida albicansSRR30894133SRR30894143459
Candida albicansSRR30894133SRR30894145259
Candida albicansSRR30894133SRR30894146159
Candida albicansSRR30894133SRR30894147359
Candida albicansSRR30894133SRR33417537859
Candida albicansSRR30894133SRR33417538959
Candida albicansSRR30894133SRR33417540359
Candida albicansSRR30894133SRR33417541259
Candida albicansSRR30894133SRR33417544859
Candida albicansSRR30894133SRR334175451659
Candida albicansSRR30894135SRR30894138459
Candida albicansSRR30894135SRR30894139459
Candida albicansSRR30894135SRR30894141659
Candida albicansSRR30894135SRR30894142659
Candida albicansSRR30894135SRR308941431059
Candida albicansSRR30894135SRR30894145859
Candida albicansSRR30894135SRR30894146759
Candida albicansSRR30894135SRR30894147959
Candida albicansSRR30894135SRR33417537859
Candida albicansSRR30894135SRR334175381559
Candida albicansSRR30894135SRR33417540959
Candida albicansSRR30894135SRR33417541859
Candida albicansSRR30894135SRR33417544859
Candida albicansSRR30894135SRR334175452059
Candida albicansSRR30894138SRR30894139059
Candida albicansSRR30894138SRR30894141259
Candida albicansSRR30894138SRR30894142259
Candida albicansSRR30894138SRR30894143659
Candida albicansSRR30894138SRR30894145459
Candida albicansSRR30894138SRR30894146359
Candida albicansSRR30894138SRR30894147559
Candida albicansSRR30894138SRR33417537459
Candida albicansSRR30894138SRR334175381159
Candida albicansSRR30894138SRR33417540559
Candida albicansSRR30894138SRR33417541459
Candida albicansSRR30894138SRR33417544459
Candida albicansSRR30894138SRR334175451859
Candida albicansSRR30894139SRR30894141259
Candida albicansSRR30894139SRR30894142259
Candida albicansSRR30894139SRR30894143659
Candida albicansSRR30894139SRR30894145459
Candida albicansSRR30894139SRR30894146359
Candida albicansSRR30894139SRR30894147559
Candida albicansSRR30894139SRR33417537459
Candida albicansSRR30894139SRR334175381159
Candida albicansSRR30894139SRR33417540559
Candida albicansSRR30894139SRR33417541459
Candida albicansSRR30894139SRR33417544459
Candida albicansSRR30894139SRR334175451859
Candida albicansSRR30894141SRR30894142059
Candida albicansSRR30894141SRR30894143459
Candida albicansSRR30894141SRR30894145259
Candida albicansSRR30894141SRR30894146159
Candida albicansSRR30894141SRR30894147359
Candida albicansSRR30894141SRR33417537659
Candida albicansSRR30894141SRR33417538959
Candida albicansSRR30894141SRR33417540359
Candida albicansSRR30894141SRR33417541259
Candida albicansSRR30894141SRR33417544659
Candida albicansSRR30894141SRR334175451659
Candida albicansSRR30894142SRR30894143459
Candida albicansSRR30894142SRR30894145259
Candida albicansSRR30894142SRR30894146159
Candida albicansSRR30894142SRR30894147359
Candida albicansSRR30894142SRR33417537659
Candida albicansSRR30894142SRR33417538959
Candida albicansSRR30894142SRR33417540359
Candida albicansSRR30894142SRR33417541259
Candida albicansSRR30894142SRR33417544659
Candida albicansSRR30894142SRR334175451659
Candida albicansSRR30894143SRR30894145459
Candida albicansSRR30894143SRR30894146359
Candida albicansSRR30894143SRR30894147559
Candida albicansSRR30894143SRR334175371059
Candida albicansSRR30894143SRR334175381159
Candida albicansSRR30894143SRR33417540559
Candida albicansSRR30894143SRR33417541459
Candida albicansSRR30894143SRR334175441059
Candida albicansSRR30894143SRR334175451859
Candida albicansSRR30894145SRR30894146159
Candida albicansSRR30894145SRR30894147359
Candida albicansSRR30894145SRR33417537859
Candida albicansSRR30894145SRR33417538959
Candida albicansSRR30894145SRR33417540359
Candida albicansSRR30894145SRR33417541259
Candida albicansSRR30894145SRR33417544859
Candida albicansSRR30894145SRR334175451659
Candida albicansSRR30894146SRR30894147259
Candida albicansSRR30894146SRR33417537759
Candida albicansSRR30894146SRR33417538859
Candida albicansSRR30894146SRR33417540259
Candida albicansSRR30894146SRR33417541159
Candida albicansSRR30894146SRR33417544759
Candida albicansSRR30894146SRR334175451559
Candida albicansSRR30894147SRR33417537959
Candida albicansSRR30894147SRR334175381059
Candida albicansSRR30894147SRR33417540459
Candida albicansSRR30894147SRR33417541359
Candida albicansSRR30894147SRR33417544959
Candida albicansSRR30894147SRR334175451759
Candida albicansSRR33417537SRR334175381559
Candida albicansSRR33417537SRR33417540959
Candida albicansSRR33417537SRR33417541859
Candida albicansSRR33417537SRR33417544059
Candida albicansSRR33417537SRR334175452259
Candida albicansSRR33417538SRR334175401059
Candida albicansSRR33417538SRR33417541959
Candida albicansSRR33417538SRR334175441559
Candida albicansSRR33417538SRR334175452359
Candida albicansSRR33417540SRR33417541359
Candida albicansSRR33417540SRR33417544959
Candida albicansSRR33417540SRR334175451759
Candida albicansSRR33417541SRR33417544859
Candida albicansSRR33417541SRR334175451659
Candida albicansSRR33417544SRR334175452259
Candida tropicalisSRR30894136SRR308941441897923707
Candida tropicalisSRR30894136SRR334175421879923707
Candida tropicalisSRR30894136SRR334175431880123707
Candida tropicalisSRR30894144SRR3341754294023707
Candida tropicalisSRR30894144SRR3341754394423707
Candida tropicalisSRR33417542SRR334175431523707
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
rMAP-Myc-Candida | Rapid Mycological Analysis Pipeline for Candida