TB-Profiler result

Run: ERR13266892
Summary

Run ID: ERR13266892

Sample name:

Date: 2025-02-11T16:32:37.600785

Number of reads: 1960146

Percentage reads mapped: 99.24

Median coverage: 56.0

Strain: lineage3.1.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.98
lineage3.1.2 East-African-Indian RD750 0.98
lineage3.1 East-African-Indian RD750 0.96
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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
pyrazinamide
streptomycin rrs n.462C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid Assoc w R High-level resistance
embA 4243217 c.-16C>T upstream_gene_variant 0.98 ethambutol Uncertain significance Mutation from literature
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
gyrA 7585 p.Ser95Thr missense_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9122 c.1821C>T synonymous_variant 0.97 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
hadA 731920 c.-10T>C upstream_gene_variant 1.0 isoniazid Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.98 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764581 c.1212T>C synonymous_variant 0.13 rifampicin
rpoC 764611 c.1242G>C synonymous_variant 0.14 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764681 c.1312C>T synonymous_variant 0.16 rifampicin
rpoC 764713 c.1344G>A synonymous_variant 0.16 rifampicin
rpoC 764716 c.1347G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764746 c.1377G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764758 c.1389C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764817 p.Val483Gly missense_variant 0.91 rifampicin Uncertain significance
rpoC 766843 c.3474T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 766861 c.3492G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.19 rifampicin
rpoC 766894 c.3525T>C synonymous_variant 0.18 rifampicin
rpoC 766895 c.3526T>C synonymous_variant 0.18 rifampicin
rpoC 766900 c.3531T>C synonymous_variant 0.18 rifampicin
rpoC 766918 c.3549C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 766933 c.3564A>G synonymous_variant 0.2 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.24 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.21 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.18 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
embR 1417933 c.-586G>T upstream_gene_variant 0.95 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472300 n.455C>T non_coding_transcript_exon_variant 0.25 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rpsA 1833802 c.261A>G synonymous_variant 0.17 pyrazinamide
rpsA 1833811 c.270G>T synonymous_variant 0.16 pyrazinamide
rpsA 1833820 c.279G>A synonymous_variant 0.18 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.18 pyrazinamide
rpsA 1833859 c.318C>T synonymous_variant 0.18 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.15 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.12 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.1 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 0.98 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.97 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.99 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Not assoc w R
folC 2746646 p.Gln318Pro missense_variant 1.0 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.98 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
ribD 2987588 c.750C>T synonymous_variant 0.95 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626029 c.585A>G synonymous_variant 0.1 rifampicin
bedaquiline
mtrB 3626041 c.573C>G synonymous_variant 0.12 rifampicin
bedaquiline
mtrB 3626054 p.Leu187Ser missense_variant 0.14 rifampicin
bedaquiline
mtrB 3626062 c.552T>G synonymous_variant 0.14 rifampicin
bedaquiline
mtrB 3626070 p.Ile182Val missense_variant 0.14 rifampicin
bedaquiline
mtrB 3626071 c.543C>T synonymous_variant 0.14 rifampicin
bedaquiline
mtrB 3626077 c.537C>G synonymous_variant 0.15 rifampicin
bedaquiline
mtrB 3626083 c.531G>C synonymous_variant 0.16 rifampicin
bedaquiline
mtrB 3626092 c.522T>C synonymous_variant 0.16 rifampicin
bedaquiline
mtrB 3626095 p.Glu173Asp missense_variant 0.17 rifampicin
bedaquiline
mtrB 3626101 p.Gln171His missense_variant 0.16 rifampicin
bedaquiline
mtrB 3626110 c.504C>G synonymous_variant 0.2 rifampicin
bedaquiline
mtrB 3626131 c.483G>C synonymous_variant 0.19 rifampicin
bedaquiline
mtrB 3626137 c.477G>A synonymous_variant 0.14 rifampicin
bedaquiline
mtrB 3626154 c.460C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626158 c.456C>T synonymous_variant 0.15 rifampicin
bedaquiline
mtrB 3626161 c.453C>G synonymous_variant 0.15 rifampicin
bedaquiline
mtrB 3626170 c.444T>C synonymous_variant 0.11 rifampicin
bedaquiline
mtrB 3626179 c.435A>C synonymous_variant 0.13 rifampicin
bedaquiline
mtrB 3626380 p.Ile78Thr missense_variant 0.13 rifampicin
bedaquiline
mtrB 3626389 p.Arg75Lys missense_variant 0.13 rifampicin
bedaquiline
mtrB 3626400 p.Ile72Val missense_variant 0.12 rifampicin
bedaquiline
mtrB 3626407 c.207C>G synonymous_variant 0.12 rifampicin
bedaquiline
mtrB 3626410 c.204T>C synonymous_variant 0.11 rifampicin
bedaquiline
mtrB 3626413 c.201T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626705 c.-92G>T upstream_gene_variant 0.12 rifampicin
bedaquiline
mtrB 3626711 c.-98T>C upstream_gene_variant 0.12 rifampicin
bedaquiline
mtrA 3626723 c.627C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626744 c.-131G>C upstream_gene_variant 0.14 rifampicin
bedaquiline
mtrB 3626750 c.-137T>C upstream_gene_variant 0.13 rifampicin
bedaquiline
mtrA 3626759 c.591T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626774 c.-163_-161delAGGinsCGT upstream_gene_variant 0.18 rifampicin
bedaquiline
mtrB 3626780 c.-167T>C upstream_gene_variant 0.17 rifampicin
bedaquiline
mtrB 3626783 c.-170C>G upstream_gene_variant 0.18 rifampicin
bedaquiline
mtrA 3626786 c.564A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626798 c.-185T>C upstream_gene_variant 0.18 rifampicin
bedaquiline
mtrB 3626804 c.-191A>C upstream_gene_variant 0.17 rifampicin
bedaquiline
mtrB 3626843 c.-230G>C upstream_gene_variant 0.11 rifampicin
bedaquiline
mtrA 3626846 c.504G>A synonymous_variant 0.12 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626858 c.-245A>G upstream_gene_variant 0.12 rifampicin
bedaquiline
mtrB 3626866 c.-253T>C upstream_gene_variant 0.16 rifampicin
bedaquiline
mtrB 3626885 c.-272A>G upstream_gene_variant 0.16 rifampicin
bedaquiline
mtrB 3626890 c.-277T>C upstream_gene_variant 0.15 rifampicin
bedaquiline
mtrA 3626912 c.438T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626930 c.-317A>G upstream_gene_variant 0.18 rifampicin
bedaquiline
mtrA 3626939 p.Glu137Asp missense_variant 0.16 rifampicin
bedaquiline
mtrB 3626942 c.-329A>C upstream_gene_variant 0.17 rifampicin
bedaquiline
clpC1 4039898 c.807C>G synonymous_variant 0.14 pyrazinamide
clpC1 4039928 c.775_777delAGCinsTCG synonymous_variant 0.16 pyrazinamide
clpC1 4039931 c.774T>C synonymous_variant 0.15 pyrazinamide
clpC1 4039937 c.768G>C synonymous_variant 0.16 pyrazinamide
clpC1 4039946 c.759A>T synonymous_variant 0.16 pyrazinamide
clpC1 4039952 c.753T>C synonymous_variant 0.16 pyrazinamide
clpC1 4039958 c.747G>C synonymous_variant 0.16 pyrazinamide
clpC1 4039964 c.741C>G synonymous_variant 0.18 pyrazinamide
clpC1 4039991 c.714G>T synonymous_variant 0.22 pyrazinamide
clpC1 4040009 c.696C>G synonymous_variant 0.22 pyrazinamide
clpC1 4040015 c.690G>T synonymous_variant 0.21 pyrazinamide
clpC1 4040018 c.687G>C synonymous_variant 0.2 pyrazinamide
clpC1 4040021 c.684A>T synonymous_variant 0.18 pyrazinamide
clpC1 4040024 c.681A>G synonymous_variant 0.19 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.22 pyrazinamide
clpC1 4040057 c.648C>T synonymous_variant 0.19 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 1.0 pyrazinamide
glpK 4138358 p.Leu466Phe missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
glpK 4138622 c.1134C>T synonymous_variant 0.95 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240190 p.Pro110Ser missense_variant 0.97 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.98 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245187 p.Thr652Lys missense_variant 0.96 ethambutol Uncertain significance
aftB 4267781 c.1056C>A synonymous_variant 0.95 ethambutol Not assoc w R - Interim
ubiA 4269719 p.Ala39Ser missense_variant 0.98 ethambutol Uncertain significance
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 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4408203 c.-1A>C upstream_gene_variant 0.97 streptomycin Uncertain significance