TB-Profiler result

Run: ERR11268038
Summary

Run ID: ERR11268038

Sample name:

Date: 2024-10-04T17:13:07.834391

Number of reads: 690621

Percentage reads mapped: 98.12

Median coverage: 32.0

Strain: La1.6

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
La1.6 M.bovis None 1.0
La1 M.bovis None 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 pncA p.His57Asp Assoc w R
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
pncA 2289073 p.His57Asp missense_variant 1.0 pyrazinamide 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 467 p.His156Arg missense_variant 1.0 isoniazid Not assoc w R
gyrB 5752 c.513G>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6406 c.1167C>T synonymous_variant 0.97 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6446 p.Ala403Ser missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrB 7042 c.1803C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7394 c.93T>C synonymous_variant 0.19 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 7397 c.96G>C synonymous_variant 0.22 levofloxacin
moxifloxacin
gyrA 7412 c.111C>G synonymous_variant 0.25 levofloxacin
moxifloxacin
gyrA 7421 c.120G>C synonymous_variant 0.27 levofloxacin
moxifloxacin
gyrA 7424 c.123G>T synonymous_variant 0.27 levofloxacin
moxifloxacin
gyrA 7427 c.126G>C synonymous_variant 0.29 levofloxacin
moxifloxacin
gyrA 7436 c.135C>G synonymous_variant 0.31 levofloxacin
moxifloxacin
gyrA 7442 c.141G>T synonymous_variant 0.31 levofloxacin
moxifloxacin
gyrA 7451 c.150C>G synonymous_variant 0.32 levofloxacin
moxifloxacin
gyrA 7457 c.156T>C synonymous_variant 0.31 levofloxacin
moxifloxacin
gyrA 7463 c.162G>C synonymous_variant 0.31 levofloxacin
moxifloxacin
gyrA 7466 c.165G>C synonymous_variant 0.31 levofloxacin
moxifloxacin
gyrA 7472 c.171T>C synonymous_variant 0.32 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 7475 c.174A>G synonymous_variant 0.31 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7480 p.Phe60Tyr missense_variant 0.3 levofloxacin
moxifloxacin
gyrA 7484 c.183T>C synonymous_variant 0.29 levofloxacin
moxifloxacin
gyrA 7496 c.195C>G synonymous_variant 0.3 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7514 c.213C>G synonymous_variant 0.29 levofloxacin
moxifloxacin
gyrA 7517 c.216G>A synonymous_variant 0.27 levofloxacin
moxifloxacin
gyrA 7520 c.219G>C synonymous_variant 0.28 levofloxacin
moxifloxacin
gyrA 7523 c.222C>A synonymous_variant 0.28 levofloxacin
moxifloxacin
gyrA 7526 c.225G>C synonymous_variant 0.27 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7559 c.258G>A synonymous_variant 0.24 levofloxacin
moxifloxacin
gyrA 7571 c.270G>C synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7574 c.273G>C synonymous_variant 0.22 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7587 c.286C>T synonymous_variant 0.22 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7592 c.291G>C synonymous_variant 0.23 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7595 c.294C>A synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 7607 c.306C>G synonymous_variant 0.19 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8285 c.984C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9143 c.1842T>C synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9217 p.Asp639Ala missense_variant 0.96 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13197 p.Thr121Ser missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13228 c.330delG frameshift_variant 1.0 isoniazid Uncertain significance
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid 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 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
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
Rv1129c 1254582 c.-48A>G upstream_gene_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.97 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
sigE 1364579 p.Asp56Gly missense_variant 1.0 pyrazinamide
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474110 n.455dupT non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474452 n.795C>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
inhA 1674480 c.279T>C synonymous_variant 0.25 isoniazid
ethionamide
inhA 1674483 c.282G>C synonymous_variant 0.25 isoniazid
ethionamide
inhA 1674486 c.285T>C synonymous_variant 0.24 isoniazid
ethionamide
inhA 1674489 c.288G>C synonymous_variant 0.24 isoniazid
ethionamide
inhA 1674507 c.306G>C synonymous_variant 0.29 isoniazid
ethionamide
inhA 1674534 c.333G>C synonymous_variant 0.27 isoniazid Not assoc w R - Interim
ethionamide
inhA 1674539 p.Tyr113Phe missense_variant 0.29 isoniazid
ethionamide
inhA 1674542 p.Ala114Glu missense_variant 0.3 isoniazid
ethionamide
inhA 1674546 c.345T>C synonymous_variant 0.3 isoniazid
ethionamide
inhA 1674549 c.348G>C synonymous_variant 0.28 isoniazid
ethionamide
inhA 1674550 p.Ser117Ala missense_variant 0.28 isoniazid
ethionamide
inhA 1674573 c.372G>C synonymous_variant 0.31 isoniazid
ethionamide
inhA 1674576 c.375T>C synonymous_variant 0.3 isoniazid
ethionamide
inhA 1674579 c.378G>C synonymous_variant 0.3 isoniazid
ethionamide
inhA 1674585 c.384T>C synonymous_variant 0.3 isoniazid
ethionamide
inhA 1674589 p.Met130Leu missense_variant 0.28 isoniazid
ethionamide
inhA 1674597 c.396G>A synonymous_variant 0.29 isoniazid
ethionamide
inhA 1674600 c.399G>C synonymous_variant 0.29 isoniazid
ethionamide
inhA 1674618 c.417C>T synonymous_variant 0.27 isoniazid
ethionamide
inhA 1674654 c.453G>C synonymous_variant 0.22 isoniazid
ethionamide
inhA 1674656 p.Ser152Thr missense_variant 0.22 isoniazid
ethionamide
inhA 1674690 c.489C>G synonymous_variant 0.2 isoniazid
ethionamide
inhA 1674693 c.492C>A synonymous_variant 0.21 isoniazid
ethionamide
inhA 1674702 c.501G>A synonymous_variant 0.19 isoniazid
ethionamide
inhA 1674703 c.502T>C synonymous_variant 0.19 isoniazid
ethionamide
inhA 1674714 c.513C>G synonymous_variant 0.18 isoniazid
ethionamide
inhA 1674718 c.517A>C synonymous_variant 0.18 isoniazid
ethionamide
inhA 1674729 c.528G>A synonymous_variant 0.17 isoniazid
ethionamide
inhA 1674745 p.Tyr182Val missense_variant 0.15 isoniazid
ethionamide
inhA 1674750 c.549T>C synonymous_variant 0.15 isoniazid
ethionamide
inhA 1674756 c.555T>G synonymous_variant 0.15 isoniazid
ethionamide
inhA 1674765 c.564C>G synonymous_variant 0.19 isoniazid
ethionamide
inhA 1674774 c.573A>C synonymous_variant 0.17 isoniazid
ethionamide
inhA 1674777 c.576C>G synonymous_variant 0.2 isoniazid
ethionamide
inhA 1674780 c.579T>G synonymous_variant 0.17 isoniazid
ethionamide
rpsA 1834633 c.1092A>G synonymous_variant 0.24 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.24 pyrazinamide
rpsA 1834666 c.1125G>C synonymous_variant 0.24 pyrazinamide
rpsA 1834667 p.Ala376Ser missense_variant 0.24 pyrazinamide
rpsA 1834690 c.1149T>C synonymous_variant 0.19 pyrazinamide
rpsA 1834859 p.Ala440Thr missense_variant 1.0 pyrazinamide Uncertain significance
tsnR 1854289 c.684C>T synonymous_variant 1.0 linezolid
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
bacA 2062922 p.Ile603Val missense_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2064293 p.Thr146Ala missense_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
ndh 2102121 p.Asp308Asn missense_variant 1.0 isoniazid
delamanid
ethionamide
ndh 2103173 c.-132delG upstream_gene_variant 1.0 isoniazid
delamanid
ethionamide
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 1.0 isoniazid Not assoc w R
katG 2156025 c.87C>A synonymous_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168011 p.Ser868Arg missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168319 p.Thr765Ile missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168814 c.1798dupA frameshift_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223062 p.Thr35Ala 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
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
folC 2746245 p.Ala452Thr missense_variant 1.0 para-aminosalicylic_acid
Rv2477c 2782927 c.1116A>G synonymous_variant 1.0 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R - Interim
ribD 2987615 c.777A>G stop_lost&splice_region_variant 1.0 para-aminosalicylic_acid
Rv2681 2997325 p.Ala196Val missense_variant 1.0 capreomycin Uncertain significance
ald 3086728 c.-92C>T upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 1.0 cycloserine
Rv3083 3448783 p.Val94Ile missense_variant 1.0 ethionamide Uncertain significance
Rv3236c 3612505 c.612T>C synonymous_variant 1.0 pyrazinamide
lpqB 3623730 p.Ser394Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3624350 c.561G>T synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.97 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3624593 c.318G>A synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624710 c.201G>A synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878630 c.-124delC upstream_gene_variant 1.0 rifampicin Not assoc w R
clpC1 4038403 c.2302T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242970 c.3108C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246551 p.Asn13Ser missense_variant 1.0 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
embB 4247791 c.1278C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
aftB 4267858 p.Ile327Val missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_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 4408265 c.-63T>C upstream_gene_variant 0.97 streptomycin