rMAP-Myc-Candida report

Samples analyzed2

Top species groups2

Total AMR hits1

Median N5061,358

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

Nakaseomyces glabratus

2. Surveillance readiness and interpretation dashboard

This integrated table combines species confidence, QUAST assembly-contiguity metrics, AMR marker status, phylogeny eligibility, and optional metadata into a practical surveillance-readiness view.

Sample	Collection date	site	species	Species confidence	Assembly QC	QUAST contiguity QC	AMR screen	Phylogeny	Surveillance status	Reason / note
ERR263534	NA	NA	Candida albicans	High	Pass	Pass	1 marker(s)	Excluded	Review	AMR marker detected
ERR331060	NA	NA	Nakaseomyces glabratus	Low / review	Pass	Pass	No curated marker detected	Excluded	Review	species confidence

3. Surveillance metadata

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

4. Sample-level surveillance summary

ERR263534

Candida albicans Review

Species reads99.62%

Contigs1,222

N5056,305

GC (%)33.42

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

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

ERR331060

Nakaseomyces glabratus Review

Species reads73.73%

Contigs430

N5066,410

GC (%)38.08

No curated genomic AMR marker detected — not susceptible Species confidence: Low / review Phylogeny: Excluded

Interpretation: species confidence. Species note: Top species abundance <80%; possible mixed sample, contamination, or weak species assignment. Phylogeny note: Requires at least 3 samples for a species-specific tree.

5. Candida species typing using Kraken2/Bracken

Top species calls are derived from the custom Candida-focused Kraken2/Bracken database bundled in the species-typing Docker image.

Sample	Top species	Reads (%)	clade_reads	taxon_reads	taxid	evidence
ERR263534	Candida albicans	99.62%	2,597,985	2,597,985	5476	Bracken species-level abundance
ERR331060	Nakaseomyces glabratus	73.73%	190,342	190,342	5478	Bracken species-level abundance

6. MEGAHIT assembly summary

Sample	contigs	Total bp	N50	Largest contig
ERR263534	1,222	14,775,901	56,305	246,808
ERR331060	430	11,615,102	66,410	166,550

7. Assembly quality assessment with QUAST

QUAST values are parsed from the native per-sample report.tsv format and transposed into one row per sample. This default surveillance mode reports QUAST assembly contiguity metrics such as contig count, total length, N50, largest contig, and GC percentage. It is very fast. BUSCO and Compleasm tasks are available as optional modules, but they are disabled by default in the recommended JSON and are not required for this QUAST-based assembly assessment.

Sample	# contigs	Largest contig	Total length	GC (%)	N50
ERR263534	1,222	246,808	14,775,901	33.42	56,305
ERR331060	430	166,550	11,615,102	38.08	66,410

8. Fungal antifungal-resistance characterization

This section reports mutation/gene-level evidence emitted by the configured fungal AMR container. A “No marker detected” result is not a susceptible call. Fluconazole resistance can be caused by ERG11 alterations, TAC1/UPC2/MRR1/PDR1-mediated efflux, aneuploidy/LOH, copy-number changes, species-specific mechanisms, or markers absent from the current AMR database.

Sample	species	drug_class	drug	Gene / status	mutation	effect	evidence_level	interpretation
ERR263534	Candida albicans	azole	fluconazole/other azoles	Cyp51	V437I	FungAMR MUTATION	FungAMR curated marker detected by ChroQueTas	Curated ChroQueTas/FungAMR marker detected: Cyp51 V437I (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(8/-2),Isavuconazole(8/NA),Itraconazole(8/-8),Posaconazole(8/NA),Voriconazole(8/-8). Source: amr_out/ERR263534.ChroQueTas/ERR263534.contigs.ChroQueTaS.Cyp51.1.tsv:437
ERR331060	Nakaseomyces glabratus	azole/other	fluconazole/other	No marker — not susceptible	NA	NA	scanner_detected_candidate_marker	The AMR scanner produced text consistent with a possible curated resistance marker, but rc151 could not parse an exact ChroQueTas marker row. Review fungal_amr.raw.tsv and fungal_amr.log for the exact record: amr_out/ERR331060.ChroQueTas.AMR_summary.tsv No AMR mutations found in ERR331060.contigs

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 albicans	SKIPPED_TOO_FEW_SAMPLES	1	snippy_core	1	NA	Requires at least 3 samples for a species-specific tree.
Nakaseomyces glabratus	SKIPPED_TOO_FEW_SAMPLES	1	haploid_bcftools_consensus	1	NA	Requires at least 3 samples for a species-specific tree.

Species without a displayed tree:

Candida albicans: SKIPPED_TOO_FEW_SAMPLES; samples after species-specific consensus/eligibility = 1; branch = snippy_core; note = Requires at least 3 samples for a species-specific tree.
Nakaseomyces glabratus: SKIPPED_TOO_FEW_SAMPLES; samples after species-specific consensus/eligibility = 1; branch = haploid_bcftools_consensus; note = Requires at least 3 samples for a species-specific tree.

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

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

No core-SNP alignment was available for pairwise SNP-distance calculation.

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.

Integrated Candida fungal genomics report