Mycobacterium tuberculosis Genotyping Run Report

Results generated through the wf-tb-amr Nextflow workflow provided by Oxford Nanopore Technologies.

RUO

This report is intended for RESEARCH USE ONLY. Oxford Nanopore Technologies & Oxford Nanopore Diagnostics products are not intended for use for health assessment or to diagnose, treat, mitigate, cure or prevent any disease or condition.

Run Controls

No Template Controls

blank

Based on set thresholds this sample Passed
Any sample labelled as no_template_control on the sample sheet are subject to thresholds (>=20 reads in >3 targets = fail) which determine test validity. Multiple no_template_control samples can be used.
Positive Controls

positive

Based on set thresholds this sample Passed
embB 16
Any sample labelled as positive_control on the sample sheet are subject to thresholds (<-20 reads in >2 targets = fail) which determine test validity. Multiple positive_control samples can be used .

Results Summary

Presence/Absence of TB
TB present TB present but targets missing TB absent or present below limit of detection
Based on set thresholds (>=-20 reads in >8 targets) this section describes whether TB is likely present, absent or present below the limit of detection.
Antimicrobial Resistance

This section summarises the antibiotic resistance assignment per sample. Resistance calls are included for Groups 1 (associated with resistance) and 2 (associated with resistance (interim)) and those classfied as ONT as 'likely to cause resistance'. For further information on the justiciation and confidence of these antibiotic assignments, please review following sections in the report.

Interpretation:
  • Resistant (Group 1)
  • Resistant (Group 2)
  • Resistant (ONT)
  • No Resistance Detected
  • Undetermined

Number of Reads Per Sample

Sample Details
The tabular information below shows a summary of the genetic variants observed within the sample. Data included in the table includes genomic coordinates, HGVS protein and nucleotide, the drug resistance the variant confers, the allele frequency of the variant (AF) and the phred scaled fishers exact p value of strand bias (FS_SB).
blank (barcode95) no_template_control
Variants Summary
This table contains all variants classified by the WHO as Group 1 (associated with resistance - indicated with (1) ) or Group 2 (associated with resistance (interim) - indicated with (2)) and those classfied as ONT as likely to cause resistance, indicated by (ONT)
chromosome position reference alternate HGVS_NUCLEOTIDE HGVS_PROTEIN GENE ANTIBIOTICS AF FS_SB
Target Coverage by Strand
Note that the position co-ordiante is discretized by 20 bases. 20 bases.
positive (barcode93) positive_control
Variants Summary
This table contains all variants classified by the WHO as Group 1 (associated with resistance - indicated with (1) ) or Group 2 (associated with resistance (interim) - indicated with (2)) and those classfied as ONT as likely to cause resistance, indicated by (ONT)
chromosome position reference alternate HGVS_NUCLEOTIDE HGVS_PROTEIN GENE ANTIBIOTICS AF FS_SB
Target Coverage by Strand
Note that the position co-ordiante is discretized by 20 bases. 20 bases.
sample1 (barcode92) test_sample
Variants Summary
This table contains all variants classified by the WHO as Group 1 (associated with resistance - indicated with (1) ) or Group 2 (associated with resistance (interim) - indicated with (2)) and those classfied as ONT as likely to cause resistance, indicated by (ONT)
chromosome position reference alternate HGVS_NUCLEOTIDE HGVS_PROTEIN GENE ANTIBIOTICS AF FS_SB
NC_000962.3 7581 G C c.280G>C p.Asp94His gyrA LEV (1),MXF (1) 0.940741 -0.00
NC_000962.3 761155 C T c.1349C>T p.Ser450Leu rpoB RIF (1) 0.917051 5.38
NC_000962.3 781822 A G c.263A>G p.Lys88Arg rpsL STM (1) 0.840580 3.74
NC_000962.3 1674048 G A c.609G>A p.Leu203Leu fabG1 INH (1),ETH (2) 0.888889 -0.00
NC_000962.3 2155168 C G c.944G>C p.Ser315Thr katG INH (1) 0.987220 5.96
NC_000962.3 2289213 T G c.29A>C p.Gln10Pro pncA PZA (1) 0.942731 10.54
NC_000962.3 2715342 C T c.-10G>A None eis KAN (1) 0.932862 14.06
NC_000962.3 4247730 G C c.1217G>C p.Gly406Ala embB EMB (1) 0.915966 10.37
Target Coverage by Strand
Note that the position co-ordiante is discretized by 20 bases. 20 bases.
sample2 (barcode94) test_sample
Target Coverage by Strand
Note that the position co-ordiante is discretized by 20 bases. 20 bases.

Assay Details

full-name group drug-class who-class line in-assay genes short-name
kanamycin None injectable None second-line True eis,rrs KAN
amikacin None injectable None second-line True rrs AMI
capreomycin None injectable None first-line True gidB,rrs,tlyA CAP
ciprofloxacin None fluoroquinolones None second-line False CIP
ethionamide None None None second-line True ethA,fabG1,inhA ETH
prothionamide None None None second-line False PTH
ethambutol None None None first-line True embB EMB
isoniazid None None None first-line True fabG1,inhA,katG INH
rifampicin None None None first-line True rpoB RIF
pyrazinamide None None None first-line True pncA PZA
bedaquiline A None None second-line True Rv0678 BDQ
linezolid A None None second-line True rplC,rrl LZD
clofazamine None None None second-line True Rv0678 CFZ
moxifloxacin A fluoroquinolones None second-line True gyrA MXF
levofloxacin A fluoroquinolones None second-line True gyrA LEV
delamanid None None None none False DLM
streptomycin None None None second-line True gidB,rpsL,rrs STM

Software versions

The table below highlights versions of key software used within the analysis.

Name Version
minimap2 2.23-r1111
samtools 1.12
bedtools v2.30.0
bcftools 1.12

Workflow parameters

The table below highlights values of the main parameters used in this analysis.

Key Value
help False
version False
analyse_unclassified False
out_dir wf-tb-amr
fastq test_data/fastq
sample None
sample_sheet test_data/sample_sheet.csv
align_threads 4
mpileup_threads 4
maf 0.1
strand_bias 1000
minimum_read_support 5
downsample None
ntc_threshold 20,3
sample_threshold -20,8
positive_threshold -20,2
disable_ping False
aws_image_prefix None
aws_queue None
monochrome_logs False
validate_params True
show_hidden_params False
schema_ignore_params show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wf
wf {'example_cmd': ['--fastq wf-tb-amr-demo/fastq', '--sample_sheet wf-tb-amr-demo/sample_sheet.csv'], 'agent': 'cw-ci', 'container_sha': 'sha837f62ff13f7f65a6d58f4d0aff6a9f86dda6fb7', 'common_sha': 'sha91452ece4f647f62b32dac3a614635a6f0d7f8b5'}
_reference /builds/zdQY-a-d/0/epi2melabs/workflows/wf-tb-amr/./data/primer_schemes/V3/NC_000962.3.fasta
_variant_db /builds/zdQY-a-d/0/epi2melabs/workflows/wf-tb-amr/./data/primer_schemes/V3/variant_db.sorted.normalised.vcf.gz
_genbank /builds/zdQY-a-d/0/epi2melabs/workflows/wf-tb-amr/./data/primer_schemes/V3/NC_000962.3.gb
_amplicons_bed /builds/zdQY-a-d/0/epi2melabs/workflows/wf-tb-amr/./data/primer_schemes/V3/TB_amplicons.bed
_report_config /builds/zdQY-a-d/0/epi2melabs/workflows/wf-tb-amr/./data/primer_schemes/V3/report_config.eng.json

About

This report was produced using the epi2me-labs/wf-tb-amr. The workflow can be run using nextflow epi2me-labs/wf-tb-amr --help

Version details Revision: null Git Commit: null

Oxford Nanopore Technologies products are not intended for use for health assessment or to diagnose, treat, mitigate, cure or prevent any disease or condition.