TB-Profiler result

Run: SRR29096291
Summary

Run ID: SRR29096291

Sample name:

Date: 2025-02-11T17:36:42.463258

Number of reads: 1944075

Percentage reads mapped: 95.73

Median coverage: 60.0

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 0.99
lineage2.2 East-Asian (Beijing) RD105;RD207 0.99
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 1.0 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 491556 c.774G>A synonymous_variant 0.94 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
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 760370 c.564C>G synonymous_variant 0.2 rifampicin
rpoB 760679 c.873A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760765 p.Glu320Ala missense_variant 0.15 rifampicin
rpoB 760787 c.981G>C synonymous_variant 0.14 rifampicin
rpoB 760796 c.990A>G synonymous_variant 0.15 rifampicin
rpoB 760805 c.999G>C synonymous_variant 0.17 rifampicin
rpoB 760817 c.1011A>G synonymous_variant 0.17 rifampicin
rpoB 760820 c.1014T>C synonymous_variant 0.17 rifampicin
rpoB 760826 c.1020C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760841 c.1035T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760845 p.Thr347Ala missense_variant 0.18 rifampicin
rpoB 760859 c.1053T>C synonymous_variant 0.19 rifampicin
rpoB 760862 c.1056G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760869 p.Val355Thr missense_variant 0.18 rifampicin
rpoB 760886 c.1080A>G synonymous_variant 0.19 rifampicin
rpoB 760925 c.1119T>C synonymous_variant 0.16 rifampicin
rpoB 760928 c.1122G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760934 c.1128C>T synonymous_variant 0.17 rifampicin
rpoB 760946 c.1140A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760985 c.1179G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760991 c.1185G>C synonymous_variant 0.15 rifampicin
rpoB 761561 c.1755C>G synonymous_variant 0.17 rifampicin
rpoB 761564 c.1758G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761570 c.1764T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761573 c.1767C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761606 c.1800C>G synonymous_variant 0.18 rifampicin
rpoB 761612 c.1806G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761885 c.2079T>C synonymous_variant 0.2 rifampicin
rpoB 761909 c.2103T>C synonymous_variant 0.18 rifampicin
rpoB 761912 c.2106T>C synonymous_variant 0.18 rifampicin
rpoB 761915 p.Asp703Glu missense_variant 0.18 rifampicin
rpoB 761916 p.Asp704Asn missense_variant 0.18 rifampicin
rpoB 761948 c.2142G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761954 c.2148C>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 761999 c.2193G>C synonymous_variant 0.19 rifampicin
rpoB 762008 c.2202C>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 762014 c.2208C>T synonymous_variant 0.2 rifampicin
rpoB 762017 c.2211A>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 762053 c.2247T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762062 c.2256T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764888 c.1519T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764893 c.1524T>C synonymous_variant 0.17 rifampicin
rpoC 766408 c.3039C>G synonymous_variant 0.15 rifampicin
rpoC 766411 c.3042C>G synonymous_variant 0.16 rifampicin
rpoC 766426 c.3057C>T synonymous_variant 0.16 rifampicin
rpoC 766447 c.3078T>C synonymous_variant 0.21 rifampicin
rpoC 766483 c.3114G>C synonymous_variant 0.23 rifampicin
rpoC 766484 p.Val1039Ile missense_variant 0.23 rifampicin Uncertain significance
rpoC 766492 c.3123T>C synonymous_variant 0.26 rifampicin
rpoC 766528 c.3159T>C synonymous_variant 0.25 rifampicin
rpoC 766531 c.3162G>C synonymous_variant 0.21 rifampicin
rpoC 766540 p.Asp1057Glu missense_variant 0.2 rifampicin
rpoC 766573 c.3204T>C synonymous_variant 0.2 rifampicin
rpoC 766582 c.3213C>G synonymous_variant 0.15 rifampicin
rpoC 766597 c.3228C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766738 c.3369G>C synonymous_variant 0.18 rifampicin
rpoC 766750 c.3381C>G synonymous_variant 0.19 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.2 rifampicin
rpoC 766801 c.3432C>G synonymous_variant 0.21 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 766831 c.3462C>A synonymous_variant 0.24 rifampicin
rpoC 766834 c.3465G>A synonymous_variant 0.26 rifampicin
rpoC 766861 c.3492G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.21 rifampicin
rpoC 766894 c.3525T>C synonymous_variant 0.21 rifampicin
rpoC 766895 c.3526T>C synonymous_variant 0.23 rifampicin
rpoC 766900 c.3531T>C synonymous_variant 0.22 rifampicin
rpoC 766918 c.3549C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 766933 c.3564A>G synonymous_variant 0.22 rifampicin
rpoC 766945 c.3576A>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.16 rifampicin
rpoC 766978 c.3609C>A synonymous_variant 0.18 rifampicin
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 781631 c.72G>C synonymous_variant 0.15 streptomycin
rpsL 781655 c.96T>C synonymous_variant 0.16 streptomycin
rpsL 781700 c.141G>C synonymous_variant 0.23 streptomycin
rpsL 781703 c.144G>T synonymous_variant 0.25 streptomycin
rpsL 781715 c.156T>C synonymous_variant 0.22 streptomycin
rpsL 781728 c.169T>C synonymous_variant 0.2 streptomycin
rpsL 781736 c.177T>C synonymous_variant 0.17 streptomycin
rpsL 781742 c.183C>T synonymous_variant 0.18 streptomycin
rpsL 781748 c.189C>G synonymous_variant 0.19 streptomycin
rpsL 781754 c.195G>C synonymous_variant 0.21 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.21 streptomycin
rpsL 781772 c.213C>T synonymous_variant 0.23 streptomycin Not assoc w R - Interim
rpsL 781808 c.249C>T synonymous_variant 0.19 streptomycin
rpsL 781811 c.252C>T synonymous_variant 0.2 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.23 streptomycin
rpsL 781838 c.279G>C synonymous_variant 0.19 streptomycin
rpsL 781841 c.282C>G synonymous_variant 0.16 streptomycin
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
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.45 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.42 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
inhA 1674210 c.9A>C synonymous_variant 1.0 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
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 2154296 p.Ala606Pro missense_variant 0.98 isoniazid Uncertain significance
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 2222425 p.Ala247Gly missense_variant 1.0 bedaquiline
clofazimine
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
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 0.98 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626840 c.-227C>G upstream_gene_variant 0.17 rifampicin
bedaquiline
mtrA 3626846 c.504G>A synonymous_variant 0.17 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626852 c.-239G>A upstream_gene_variant 0.17 rifampicin
bedaquiline
mtrB 3626858 c.-245A>G upstream_gene_variant 0.15 rifampicin
bedaquiline
mtrB 3626861 c.-248C>G upstream_gene_variant 0.15 rifampicin
bedaquiline
mtrB 3626876 c.-263A>G upstream_gene_variant 0.15 rifampicin
bedaquiline
mtrB 3626885 c.-272A>C upstream_gene_variant 0.15 rifampicin
bedaquiline
clpC1 4038596 c.2109A>G synonymous_variant 0.18 pyrazinamide
clpC1 4038623 c.2082A>G synonymous_variant 0.17 pyrazinamide
clpC1 4038640 p.Asp689Asn missense_variant 0.18 pyrazinamide
clpC1 4038653 c.2052C>T synonymous_variant 0.18 pyrazinamide
clpC1 4038658 p.Lys683Gln missense_variant 0.18 pyrazinamide
clpC1 4038661 p.Ser682Thr missense_variant 0.19 pyrazinamide
clpC1 4038662 c.2043T>C synonymous_variant 0.2 pyrazinamide
clpC1 4038671 c.2034T>C synonymous_variant 0.19 pyrazinamide
clpC1 4038683 c.2022T>C synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
clpC1 4038695 c.2010C>G synonymous_variant 0.17 pyrazinamide
clpC1 4038755 c.1950G>C synonymous_variant 0.17 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.2 pyrazinamide
clpC1 4038782 c.1923G>C synonymous_variant 0.21 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
clpC1 4038812 c.1893T>C synonymous_variant 0.2 pyrazinamide
clpC1 4038851 c.1854G>A synonymous_variant 0.18 pyrazinamide
clpC1 4038860 c.1845G>C synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
clpC1 4038878 c.1827A>G synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4038908 c.1797C>G synonymous_variant 0.15 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.15 pyrazinamide
clpC1 4038923 c.1782A>G synonymous_variant 0.14 pyrazinamide
clpC1 4039064 c.1641C>T synonymous_variant 0.19 pyrazinamide
clpC1 4039097 c.1608G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039103 c.1602T>C synonymous_variant 0.15 pyrazinamide
clpC1 4039106 c.1599G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039112 c.1593C>G synonymous_variant 0.14 pyrazinamide
clpC1 4039391 c.1314T>G synonymous_variant 0.15 pyrazinamide
clpC1 4039412 c.1293T>G synonymous_variant 0.14 pyrazinamide
clpC1 4039415 p.Glu430Asp missense_variant 0.15 pyrazinamide Uncertain significance
clpC1 4039430 c.1275T>C synonymous_variant 0.15 pyrazinamide
clpC1 4039466 c.1239T>C synonymous_variant 0.16 pyrazinamide
clpC1 4039469 c.1236T>C synonymous_variant 0.15 pyrazinamide
clpC1 4039481 c.1224T>C synonymous_variant 0.17 pyrazinamide
clpC1 4039484 c.1221T>C synonymous_variant 0.18 pyrazinamide
clpC1 4039517 c.1188C>G synonymous_variant 0.2 pyrazinamide
clpC1 4039556 c.1149G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039559 c.1146C>G synonymous_variant 0.15 pyrazinamide
clpC1 4039565 c.1140G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039576 p.Ala377Pro missense_variant 0.15 pyrazinamide
clpC1 4039577 c.1128T>C synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4039589 c.1116G>C synonymous_variant 0.16 pyrazinamide
clpC1 4039592 c.1113G>C synonymous_variant 0.17 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 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