TB-Profiler result

Run: SRR10380045
Summary

Run ID: SRR10380045

Sample name:

Date: 2024-04-16T07:53:56.365505

Number of reads: 2619403

Percentage reads mapped: 99.61

Median coverage: 83.0

Strain: lineage4.3.4.2;lineage4.8

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.9
lineage4.3.4 Euro-American (LAM) RD174 0.09
lineage4.3.4.2 Euro-American (LAM) RD174 0.05
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide pncA p.Ala143Thr Uncertain significance Mutation from literature
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
katG 2155168 p.Ser315Thr missense_variant 0.12 isoniazid Assoc w R High-level resistance
pncA 2288815 p.Ala143Thr missense_variant 0.13 pyrazinamide Uncertain significance Mutation from literature
eis 2715342 c.-10G>A upstream_gene_variant 0.17 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13640 c.-82T>C upstream_gene_variant 0.91 isoniazid Uncertain significance
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.97 ethionamide Uncertain significance
rpoC 764840 p.Ile491Val missense_variant 0.11 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.84 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.1 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154696 c.1416A>G synonymous_variant 0.12 isoniazid Not assoc w R - Interim
PPE35 2168149 p.Pro822Ser missense_variant 0.85 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.91 capreomycin
mtrB 3625065 p.Met517Leu missense_variant 0.14 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4248933 p.Asn807Thr missense_variant 0.89 ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R