TB-Profiler result

Run: SRR29126406
Summary

Run ID: SRR29126406

Sample name:

Date: 2025-02-11T19:12:32.690133

Number of reads: 1396086

Percentage reads mapped: 98.02

Median coverage: 42.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Sensitive

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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
isoniazid
ethambutol
pyrazinamide
streptomycin
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
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 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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
mshA 575907 p.Ala187Val missense_variant 1.0 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
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
rpoB 760655 c.849A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760661 c.855A>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327_1329delTTGinsCTC synonymous_variant 0.21 rifampicin
rpoB 761492 c.1686G>C synonymous_variant 0.19 rifampicin
rpoB 761510 c.1704T>C synonymous_variant 0.21 rifampicin
rpoB 761531 c.1725C>G synonymous_variant 0.24 rifampicin
rpoB 761537 c.1731C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 761570 c.1764T>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 761573 c.1767C>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 761606 c.1800C>G synonymous_variant 0.24 rifampicin
rpoB 761612 c.1806G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761648 c.1842T>C synonymous_variant 0.17 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763402 c.33C>G synonymous_variant 0.11 rifampicin
rpoC 764024 c.655T>C synonymous_variant 0.12 rifampicin
rpoC 764040 p.Ser224Asn missense_variant 0.14 rifampicin
rpoC 764044 c.675T>C synonymous_variant 0.13 rifampicin
rpoC 764059 c.690G>C synonymous_variant 0.16 rifampicin
rpoC 764083 c.714A>G synonymous_variant 0.16 rifampicin
rpoC 764431 c.1062G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764830 c.1461C>G synonymous_variant 0.12 rifampicin
rpoC 765751 c.2382C>G synonymous_variant 0.15 rifampicin
rpoC 765753 p.Asp795Ala missense_variant 0.15 rifampicin Uncertain significance
rpoC 765811 c.2442T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765814 c.2445A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765826 c.2457T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765835 c.2466C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765883 c.2514C>G synonymous_variant 0.16 rifampicin
rpoC 765886 c.2517C>G synonymous_variant 0.16 rifampicin
rpoC 765892 c.2523T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766672 c.3303T>C synonymous_variant 0.13 rifampicin
rpoC 766801 c.3432C>G synonymous_variant 0.13 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.12 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
mmpL5 776182 p.Asp767Asn missense_variant 1.0 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781571 c.12C>T synonymous_variant 0.15 streptomycin
rpsL 781608 p.Ser17Gly missense_variant 0.18 streptomycin
rpsL 781631 c.72G>C synonymous_variant 0.19 streptomycin
rpsL 781649 c.90T>C synonymous_variant 0.23 streptomycin
rpsL 781655 c.96T>C synonymous_variant 0.22 streptomycin
rpsL 781682 c.123T>C synonymous_variant 0.14 streptomycin
rpsL 781715 c.156T>C synonymous_variant 0.15 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.14 streptomycin
rpsL 781793 c.234G>C synonymous_variant 0.18 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.2 streptomycin
rpsL 781841 c.282C>G synonymous_variant 0.21 streptomycin
rpsL 781859 c.300T>C synonymous_variant 0.23 streptomycin Not assoc w R - Interim
rpsL 781868 c.309T>C synonymous_variant 0.22 streptomycin
rpsL 781871 c.312G>C synonymous_variant 0.22 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.31 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.26 streptomycin
rpsL 781916 c.357T>C synonymous_variant 0.28 streptomycin
rpsL 781929 p.Gly124Ser missense_variant 0.2 streptomycin Uncertain significance
rplC 800618 c.-191T>C upstream_gene_variant 0.12 linezolid
rplC 800648 c.-161A>C upstream_gene_variant 0.14 linezolid
rplC 800654 c.-155T>C upstream_gene_variant 0.16 linezolid
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
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rpsA 1833661 c.120A>G synonymous_variant 0.28 pyrazinamide
rpsA 1833667 c.126C>G synonymous_variant 0.3 pyrazinamide
rpsA 1833724 c.183C>G synonymous_variant 0.27 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.27 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.17 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.16 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.16 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.18 pyrazinamide
rpsA 1833862 c.321G>T synonymous_variant 0.25 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.25 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.24 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.24 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.24 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.22 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.22 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.99 pyrazinamide Not assoc w R - Interim
rpsA 1834195 c.654G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834201 c.660C>T synonymous_variant 0.15 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.17 pyrazinamide
rpsA 1834261 c.720A>C synonymous_variant 0.17 pyrazinamide
rpsA 1834264 c.723G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834435 c.894G>C synonymous_variant 0.18 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.11 pyrazinamide
rpsA 1834474 c.933C>G synonymous_variant 0.11 pyrazinamide
tsnR 1854169 c.564A>C synonymous_variant 1.0 linezolid 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 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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2752c 3067039 c.-848T>C upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087755 c.936G>T synonymous_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 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627068 c.282T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
bedaquiline
rpoA 3877686 c.822A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3877692 c.816G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoA 3877704 c.804G>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3877743 c.765T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877764 c.744C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3879160 c.-653A>G upstream_gene_variant 0.16 rifampicin
rpoA 3879178 c.-671T>C upstream_gene_variant 0.18 rifampicin
rpoA 3879190 c.-683C>G upstream_gene_variant 0.2 rifampicin
clpC1 4038683 c.2022T>C synonymous_variant 0.37 pyrazinamide Not assoc w R - Interim
clpC1 4038695 c.2010C>G synonymous_variant 0.37 pyrazinamide
clpC1 4038701 c.2004G>C synonymous_variant 0.37 pyrazinamide
clpC1 4038704 c.2001T>C synonymous_variant 0.36 pyrazinamide
clpC1 4038707 c.1998C>G synonymous_variant 0.36 pyrazinamide
clpC1 4038710 c.1995G>C synonymous_variant 0.36 pyrazinamide
clpC1 4038713 c.1992T>C synonymous_variant 0.37 pyrazinamide
clpC1 4038740 c.1965G>C synonymous_variant 0.28 pyrazinamide
clpC1 4038755 c.1950G>C synonymous_variant 0.26 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.27 pyrazinamide
clpC1 4038782 c.1923G>C synonymous_variant 0.22 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4038812 c.1893T>C synonymous_variant 0.21 pyrazinamide
clpC1 4038815 c.1890G>T synonymous_variant 0.21 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
clpC1 4038908 c.1797C>G synonymous_variant 0.26 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.26 pyrazinamide
clpC1 4038923 c.1782A>G synonymous_variant 0.25 pyrazinamide
clpC1 4038932 c.1773G>C synonymous_variant 0.23 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.27 pyrazinamide
clpC1 4038989 c.1716T>C synonymous_variant 0.17 pyrazinamide
clpC1 4038997 c.1708T>C synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
clpC1 4039112 c.1593C>G synonymous_variant 0.16 pyrazinamide
clpC1 4039832 c.873C>G synonymous_variant 0.11 pyrazinamide
clpC1 4039928 c.775_777delAGCinsTCG synonymous_variant 0.15 pyrazinamide
clpC1 4039931 c.774T>C synonymous_variant 0.15 pyrazinamide
clpC1 4039946 c.759A>T synonymous_variant 0.18 pyrazinamide
clpC1 4039952 c.753T>C synonymous_variant 0.13 pyrazinamide
clpC1 4039958 c.747G>C synonymous_variant 0.11 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.14 pyrazinamide
clpC1 4040036 c.669C>G synonymous_variant 0.14 pyrazinamide
clpC1 4040105 c.600C>G synonymous_variant 0.11 pyrazinamide
embC 4240780 c.918T>C synonymous_variant 0.22 ethambutol
embC 4240783 c.921G>C synonymous_variant 0.22 ethambutol
embC 4240789 c.927T>C synonymous_variant 0.24 ethambutol
embC 4240831 c.969T>G synonymous_variant 0.22 ethambutol
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 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 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R