TB-Profiler result

Run: ERR11489020
Summary

Run ID: ERR11489020

Sample name:

Date: 2024-04-15T20:35:11.798833

Number of reads: 3770037

Percentage reads mapped: 97.4

Median coverage: 114.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 1.0
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)
ethambutol embB p.Met306Val Assoc w R
pyrazinamide
streptomycin rrs n.462C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethR p.Ala95Thr Uncertain significance Mutation from literature
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 0.97 rifampicin Assoc w R
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance Mutation from literature
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 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)
embB 4247429 p.Met306Val missense_variant 0.98 ethambutol Assoc w R
ethR 4327831 p.Ala95Thr missense_variant 1.0 ethionamide 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 9304 p.Gly668Asp missense_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 1.0 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
hadA 732396 p.Gly156Ala missense_variant 0.13 isoniazid
hadA 732398 p.Ala157Thr missense_variant 0.13 isoniazid
rpoB 760283 c.477G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760298 c.492G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760310 c.504G>C synonymous_variant 0.2 rifampicin
rpoB 760328 c.522G>C synonymous_variant 0.23 rifampicin
rpoB 760331 c.525G>C synonymous_variant 0.22 rifampicin
rpoB 760340 c.534G>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 760361 c.555T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 760376 p.Asp190Glu missense_variant 0.19 rifampicin Uncertain significance
rpoB 760380 p.Thr192Leu missense_variant 0.18 rifampicin
rpoB 760406 c.600G>C synonymous_variant 0.15 rifampicin
rpoB 760412 c.606C>G synonymous_variant 0.14 rifampicin
rpoB 761314 p.Phe503Ser missense_variant 0.96 rifampicin Uncertain significance
rpoB 761891 c.2085G>C synonymous_variant 0.12 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763555 c.186C>T synonymous_variant 0.92 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763648 c.279C>T synonymous_variant 0.13 rifampicin
rpoC 763660 c.291T>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763666 c.297G>T synonymous_variant 0.16 rifampicin
rpoC 763675 c.306C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.14 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.13 rifampicin
rpoC 763735 c.366G>C synonymous_variant 0.12 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.13 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.13 rifampicin
rpoC 764257 c.888G>C synonymous_variant 0.13 rifampicin
rpoC 764266 c.897T>C synonymous_variant 0.12 rifampicin
rpoC 764269 c.900G>C synonymous_variant 0.12 rifampicin
rpoC 764278 c.909A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764872 c.1503A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764911 c.1542A>G synonymous_variant 0.12 rifampicin
rpoC 766945 c.3576A>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 766978 c.3609C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766996 c.3627C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 767035 c.3666G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 767059 c.3690T>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.19 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>A synonymous_variant 0.16 rifampicin
rpoC 767180 p.Ala1271Gln missense_variant 0.13 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 778979 c.-74G>T upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254132 p.Glu135Lys missense_variant 0.18 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475761 n.2104_2106delCGCinsGT non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.12 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1476693 n.3036G>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1476732 n.3075T>C non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154113 p.Thr667Pro missense_variant 1.0 isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2156586 c.-475T>G upstream_gene_variant 0.64 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 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
kasA 2518588 c.474T>G synonymous_variant 0.12 isoniazid
kasA 2518591 c.477G>C synonymous_variant 0.12 isoniazid
kasA 2518678 c.564C>T synonymous_variant 0.13 isoniazid
kasA 2518687 c.573C>T synonymous_variant 0.12 isoniazid
kasA 2518705 c.591T>G synonymous_variant 0.13 isoniazid
kasA 2518711 c.597A>G synonymous_variant 0.13 isoniazid
kasA 2518714 c.600A>T synonymous_variant 0.13 isoniazid
Rv2477c 2783077 c.966T>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783092 c.951A>G synonymous_variant 0.13 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin Not assoc w R - Interim
amikacin
Rv2477c 2783095 c.948C>G synonymous_variant 0.13 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R
amikacin Not assoc w R - Interim
Rv2477c 2783098 c.945C>G synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783101 c.942G>T synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783116 c.927T>C synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783140 c.903C>G synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783149 c.894G>C synonymous_variant 0.13 ethambutol
moxifloxacin Not assoc w R - Interim
streptomycin
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2783158 c.885A>C synonymous_variant 0.13 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2783182 c.861C>G synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783185 c.858G>C synonymous_variant 0.12 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783194 c.849A>G synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783221 c.822G>C synonymous_variant 0.12 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783224 c.819C>G synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783263 c.780G>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783278 c.765A>G synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783284 c.759G>C synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783289 p.Leu252Ile missense_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783299 c.744A>G synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783302 c.741A>G synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783311 c.732T>C synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783317 c.726G>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783374 c.669G>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783395 c.648T>G synonymous_variant 0.12 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038812 c.1893T>C synonymous_variant 0.15 pyrazinamide
clpC1 4038815 c.1890G>C synonymous_variant 0.16 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
clpC1 4038908 c.1797C>G synonymous_variant 0.23 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.23 pyrazinamide
clpC1 4038923 c.1780_1782delCTAinsTG frameshift_variant&synonymous_variant 0.22 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.23 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.18 pyrazinamide
clpC1 4038971 c.1734T>C synonymous_variant 0.14 pyrazinamide
clpC1 4038974 c.1731T>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4038989 c.1716T>C synonymous_variant 0.16 pyrazinamide
clpC1 4038997 c.1708T>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4039010 c.1695G>A synonymous_variant 0.15 pyrazinamide
clpC1 4039022 c.1683A>G synonymous_variant 0.14 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R