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: 2026-05-31 17:16:15 UTCRun stamp: 20260531_171615_UTCCustom Candida Kraken2/Bracken DBMEGAHIT assembly
Samples analyzed5
Top species groups1
Total AMR hits5
Median N5024,692

1. Executive summary

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

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

Species distribution

Candidozyma auris
5

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
SRR104611382018-05-160.58 N 37.84 ECandidozyma aurisHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR104612382013-10-220.58 N 37.84 ECandidozyma aurisHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR306929922019-06-25NACandidozyma aurisHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR306930122019-06-27NACandidozyma aurisHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected
SRR306930322019-06-06NACandidozyma aurisHighPassPass1 marker(s)Included / eligibleReviewAMR marker detected

3. Surveillance metadata

Samplecountrycollection_date
SRR30693032Kenya2019-06-06
SRR10461138Kenya2018-05-16
SRR10461238Kenya2013-10-22
SRR30692992Kenya2019-06-25
SRR30693012Kenya2019-06-27

4. Sample-level surveillance summary

SRR10461138

Candidozyma auris Review
Species reads99.61%
Contigs1,553
N5021,941
GC (%)44.81

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 (5 samples)

SRR10461238

Candidozyma auris Review
Species reads98.54%
Contigs1,161
N5024,815
GC (%)44.70

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 (5 samples)

SRR30692992

Candidozyma auris Review
Species reads99.05%
Contigs1,128
N5024,720
GC (%)44.74

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 (5 samples)

SRR30693012

Candidozyma auris Review
Species reads99.22%
Contigs1,087
N5024,104
GC (%)44.79

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 (5 samples)

SRR30693032

Candidozyma auris Review
Species reads98.37%
Contigs1,108
N5024,692
GC (%)44.77

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 (5 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
SRR10461138Candidozyma auris
99.61%		2,308,9542,308,954498019Bracken species-level abundance
SRR10461238Candidozyma auris
98.54%		2,808,3882,808,388498019Bracken species-level abundance
SRR30692992Candidozyma auris
99.05%		2,874,3962,874,396498019Bracken species-level abundance
SRR30693012Candidozyma auris
99.22%		2,050,1042,050,104498019Bracken species-level abundance
SRR30693032Candidozyma auris
98.37%		2,249,3962,249,396498019Bracken species-level abundance

6. MEGAHIT assembly summary

SamplecontigsTotal bpN50Largest contig
SRR104611381,55312,980,96421,94184,473
SRR104612381,16112,805,72424,81587,411
SRR306929921,12812,786,92024,720106,521
SRR306930121,08712,732,41124,104103,643
SRR306930321,10812,752,78224,692132,764

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
SRR104611381,55384,47312,980,96444.8121,941
SRR104612381,16187,41112,805,72444.7024,815
SRR306929921,128106,52112,786,92044.7424,720
SRR306930121,087103,64312,732,41144.7924,104
SRR306930321,108132,76412,752,78244.7724,692

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
SRR10461138Candidozyma aurisazolefluconazole/other azolesCyp51V125AFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated 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/SRR10461138.ChroQueTas/SRR10461138.contigs.ChroQueTaS.Cyp51.1.tsv:125
SRR10461238Candidozyma aurisazolefluconazole/other azolesCyp51V125AFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated 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/SRR10461238.ChroQueTas/SRR10461238.contigs.ChroQueTaS.Cyp51.1.tsv:125
SRR30692992Candidozyma aurisazolefluconazole/other azolesCyp51V125AFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated 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/SRR30692992.ChroQueTas/SRR30692992.contigs.ChroQueTaS.Cyp51.1.tsv:125
SRR30693012Candidozyma aurisazolefluconazole/other azolesCyp51V125AFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated 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/SRR30693012.ChroQueTas/SRR30693012.contigs.ChroQueTaS.Cyp51.1.tsv:125
SRR30693032Candidozyma aurisazolefluconazole/other azolesCyp51V125AFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated 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/SRR30693032.ChroQueTas/SRR30693032.contigs.ChroQueTaS.Cyp51.1.tsv:125

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
Candidozyma aurisPASS5snippy_core_rc170_tb_styleNA64810rc170 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

Candidozyma auris core-SNP phylogenetic tree
Phylogeny interpretation note: rMAP-Candida builds one tree per species. Mixed-species Candida phylogenies are intentionally avoided. Treat these trees as species-level genomic relatedness visualizations unless recombination filtering and epidemiologic metadata support transmission interpretation.

10. Species-aware pairwise SNP distances and closest-neighbor summary

Closest-neighbor summary

speciesSampleClosest sampleSNP distanceConservative cluster flag
Candidozyma aurisSRR10461138SRR10461238143Distinct / review with metadata
Candidozyma aurisSRR10461238SRR30692992113Distinct / review with metadata
Candidozyma aurisSRR30692992SRR30693012101Distinct / review with metadata
Candidozyma aurisSRR30693012SRR30692992101Distinct / review with metadata
Candidozyma aurisSRR30693032SRR30692992119Distinct / review with metadata

Pairwise SNP-distance matrix/table

speciesSample ASample BSNP distanceCompared core-SNP sites
Candidozyma aurisSRR10461138SRR1046123814364810
Candidozyma aurisSRR10461138SRR3069299216664810
Candidozyma aurisSRR10461138SRR3069301215664810
Candidozyma aurisSRR10461138SRR3069303217464810
Candidozyma aurisSRR10461238SRR3069299211364810
Candidozyma aurisSRR10461238SRR3069301212764810
Candidozyma aurisSRR10461238SRR3069303212664810
Candidozyma aurisSRR30692992SRR3069301210164810
Candidozyma aurisSRR30692992SRR3069303211964810
Candidozyma aurisSRR30693012SRR3069303214964810
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