rMAP-Myc-Candida report

Samples analyzed4

Top species groups1

Total AMR hits2

Median N5081,340

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

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
SRR19214212	2021-04	Lagos	Candidozyma auris	High	Review	Review	1 marker(s)	Included / eligible	Review	QUAST assembly QC; AMR marker detected
SRR19214213	2021-03	Lagos	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
SRR19214214	2021-02	Lagos	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
SRR19214215	2021-02	Lagos	Candidozyma auris	High	Pass	Pass	1 marker(s)	Included / eligible	Review	AMR marker detected

3. Surveillance metadata

Sample	country	site	collection_date	specimen_type	patient_group	ward_or_facility	sequencing_platform
SRR19214215	Nigeria	Lagos	2021-02	blood	human	Lagos	ILLUMINA; Illumina MiSeq
SRR19214212	Nigeria	Lagos	2021-04	blood	human	Lagos	ILLUMINA; Illumina MiSeq
SRR19214213	Nigeria	Lagos	2021-03	blood	human	Lagos	ILLUMINA; Illumina MiSeq
SRR19214214	Nigeria	Lagos	2021-02	blood	human	Lagos	ILLUMINA; Illumina MiSeq

4. Sample-level surveillance summary

SRR19214212

Candidozyma auris Review

Species reads98.09%

Contigs8,519

N508,028

GC (%)38.76

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

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

SRR19214213

Candidozyma auris Ready for surveillance interpretation

Species reads99.52%

Contigs286

N5084,821

GC (%)45.09

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 (4 samples)

SRR19214214

Candidozyma auris Ready for surveillance interpretation

Species reads99.23%

Contigs295

N5079,213

GC (%)45.09

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

SRR19214215

Candidozyma auris Review

Species reads98.41%

Contigs300

N5083,466

GC (%)45.03

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 (4 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
SRR19214212	Candidozyma auris	98.09%	2,142,657	2,142,657	498019	Bracken species-level abundance
SRR19214213	Candidozyma auris	99.52%	4,139,459	4,139,459	498019	Bracken species-level abundance
SRR19214214	Candidozyma auris	99.23%	3,195,831	3,195,831	498019	Bracken species-level abundance
SRR19214215	Candidozyma auris	98.41%	2,451,911	2,451,911	498019	Bracken species-level abundance

6. MEGAHIT assembly summary

Sample	contigs	Total bp	N50	Largest contig
SRR19214212	8,519	31,436,259	8,028	405,307
SRR19214213	286	12,330,599	84,821	305,683
SRR19214214	295	12,315,236	79,213	269,740
SRR19214215	300	12,358,560	83,466	474,419

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
SRR19214212	8,519	405,307	31,436,259	38.76	8,028
SRR19214213	286	305,683	12,330,599	45.09	84,821
SRR19214214	295	269,740	12,315,236	45.09	79,213
SRR19214215	300	474,419	12,358,560	45.03	83,466

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
SRR19214212	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/SRR19214212.ChroQueTas/SRR19214212.contigs.ChroQueTaS.Cyp51.1.tsv:132
SRR19214213	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/SRR19214213.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR19214213.contigs
SRR19214214	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/SRR19214214.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR19214214.contigs
SRR19214215	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/SRR19214215.ChroQueTas/SRR19214215.contigs.ChroQueTaS.Cyp51.1.tsv:132

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
Candidozyma auris	PASS	4	snippy_core_rc170_tb_style	NA	199274	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

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

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

Closest-neighbor summary

species	Sample	Closest sample	SNP distance	Conservative cluster flag
Candidozyma auris	SRR19214212	SRR19214215	225	Distinct / review with metadata
Candidozyma auris	SRR19214213	SRR19214214	235	Distinct / review with metadata
Candidozyma auris	SRR19214214	SRR19214213	235	Distinct / review with metadata
Candidozyma auris	SRR19214215	SRR19214212	225	Distinct / review with metadata

Pairwise SNP-distance matrix/table

species	Sample A	Sample B	SNP distance	Compared core-SNP sites
Candidozyma auris	SRR19214212	SRR19214213	166198	199274
Candidozyma auris	SRR19214212	SRR19214214	166208	199274
Candidozyma auris	SRR19214212	SRR19214215	225	199274
Candidozyma auris	SRR19214213	SRR19214214	235	199274
Candidozyma auris	SRR19214213	SRR19214215	166227	199274
Candidozyma auris	SRR19214214	SRR19214215	166210	199274

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.

Integrated Candida fungal genomics report