TB-Profiler result

Run: SRR29274184
Summary

Run ID: SRR29274184

Sample name:

Date: 2025-02-11T10:39:00.008159

Number of reads: 3415769

Percentage reads mapped: 99.66

Median coverage: 115.0

Strain: lineage4.1.2.1;lineage4.8

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.1
lineage4.1.2 Euro-American None 0.13
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.11
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.86
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
embB p.Met306Ile Assoc w R
p.Asp354Ala Assoc w R
pyrazinamide pncA p.Ala146Val Assoc w R
streptomycin gid p.Gln125* Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA c.1391dupA Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.92 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288805 p.Ala146Val missense_variant 0.86 pyrazinamide Assoc w R
embA 4243221 c.-12C>T upstream_gene_variant 0.18 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.88 ethambutol Assoc w R
embB 4247574 p.Asp354Ala missense_variant 0.16 ethambutol Assoc w R
ethA 4326082 c.1391dupA frameshift_variant 0.93 ethionamide Assoc w R
gid 4407830 p.Gln125* stop_gained 0.89 streptomycin Assoc w R
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
dnaA 371 p.Pro124Leu missense_variant 0.83 isoniazid Not assoc w R
dnaA 779 p.Arg260His missense_variant 0.18 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.11 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13543 p.Trp6Arg missense_variant 0.79 isoniazid Uncertain significance
rpoC 764819 p.Trp484Gly missense_variant 0.81 rifampicin Uncertain significance
rpoC 764822 p.Asp485Tyr missense_variant 0.19 rifampicin Uncertain significance
rpoC 765008 p.Leu547Val missense_variant 0.86 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.15 rifampicin Not assoc w R
rpoC 766085 p.Pro906Ala missense_variant 0.82 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
atpE 1460992 c.-53A>C upstream_gene_variant 0.79 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.82 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.19 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223233 c.-69G>C upstream_gene_variant 0.18 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3087351 p.Thr178Pro missense_variant 0.18 cycloserine
Rv3236c 3613388 c.-272C>G upstream_gene_variant 0.12 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 0.14 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840764 c.657G>C synonymous_variant 0.87 cycloserine
embC 4241539 c.1677T>C synonymous_variant 0.11 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.14 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.21 kanamycin
capreomycin
amikacin
gid 4408093 p.Gly37Ala missense_variant 0.2 streptomycin Uncertain significance