TB-Profiler result

Run: ERR9786903
Summary

Run ID: ERR9786903

Sample name:

Date: 2024-10-04T18:01:10.806156

Number of reads: 2197941

Percentage reads mapped: 99.65

Median coverage: 110.0

Strain: lineage4.3.4.1;lineage4.6.2.2;lineage6.1.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.32
lineage4.6 Euro-American None 0.42
lineage6.1.2 West-Africa 2 RD702 0.16
lineage4.6.2 Euro-American RD726 0.43
lineage4.6.2.2 Euro-American (Cameroon) RD726 0.44
lineage4.3.4.1 Euro-American (LAM) RD174 0.29
lineage4 Euro-American None 0.82
lineage4.3.4 Euro-American (LAM) RD174 0.33
lineage6 West-Africa 2 RD702 0.21
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
gyrB 6446 p.Ala403Ser missense_variant 0.11 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
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 8493 p.Leu398Phe missense_variant 0.22 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8715 p.Pro472Ser missense_variant 0.28 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9143 c.1842T>C synonymous_variant 0.21 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
Rv0010c 13460 c.99T>C synonymous_variant 0.21 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.23 isoniazid Not assoc w R
fgd1 491668 p.Lys296Glu missense_variant 0.18 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.14 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 656432 p.Gly347Ser missense_variant 0.2 ethionamide Uncertain significance
Rv0565c 656609 p.Pro288Ser missense_variant 0.18 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.3 ethionamide
rpoB 759608 c.-199C>T upstream_gene_variant 0.29 rifampicin Uncertain significance
rpoB 760855 p.Thr350Ile missense_variant 0.18 rifampicin Uncertain significance
rpoB 760969 p.Ser388Leu missense_variant 0.22 rifampicin Not assoc w R
rpoB 761723 p.Glu639Asp missense_variant 0.16 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.23 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.31 rifampicin Not assoc w R
rpoC 766231 c.2862T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 0.99 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.23 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 778298 c.183G>A synonymous_variant 0.43 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800232 c.-577G>T upstream_gene_variant 0.12 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.25 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.25 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
sigE 1364434 p.Arg8Trp missense_variant 0.26 pyrazinamide Not assoc w R
Rv1258c 1406685 p.Val219Ala missense_variant 0.18 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1416633 p.Leu239Val missense_variant 0.21 ethambutol Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.14 ethambutol
atpE 1461251 c.207G>T synonymous_variant 0.19 bedaquiline Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1674434 p.Val78Ala missense_variant 0.16 isoniazid Not assoc w R
ethionamide Uncertain significance
tsnR 1853425 c.-181A>C upstream_gene_variant 0.23 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 0.23 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063121 c.1608A>T synonymous_variant 0.31 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
bacA 2063187 c.1542C>T synonymous_variant 0.42 kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
bacA 2063303 c.1426C>T synonymous_variant 0.25 kanamycin Not assoc w R - Interim
capreomycin
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.21 isoniazid Not assoc w R
katG 2155389 c.723C>G synonymous_variant 0.41 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.3 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.19 pyrazinamide Not assoc w R
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.44 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.23 bedaquiline Not assoc w R - Interim
clofazimine 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
kasA 2518132 c.18C>T synonymous_variant 0.23 isoniazid
eis 2714167 c.1165delG frameshift_variant 0.15 kanamycin Uncertain significance
amikacin Uncertain significance
ahpC 2725957 c.-236A>T upstream_gene_variant 0.26 isoniazid
ahpC 2726323 p.Pro44Arg missense_variant 0.3 isoniazid Uncertain significance
pepQ 2859830 p.Gly197Arg missense_variant 0.32 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv2680 2996208 p.Ala35Asp missense_variant 0.42 capreomycin Uncertain significance
thyX 3067474 p.Pro158Ala missense_variant 0.54 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.36 para-aminosalicylic_acid
ald 3086728 c.-92C>T upstream_gene_variant 0.26 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.55 cycloserine
ald 3087084 c.266delA frameshift_variant 0.2 cycloserine
ald 3087518 c.699C>T synonymous_variant 0.33 cycloserine
Rv3083 3448567 p.His22Asp missense_variant 0.5 ethionamide Uncertain significance
Rv3083 3448598 p.Ile32Thr missense_variant 0.34 ethionamide Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.3 pyrazinamide Not assoc w R
Rv3236c 3612143 p.Arg325His missense_variant 0.25 pyrazinamide Uncertain significance
Rv3236c 3612571 c.546C>T synonymous_variant 0.48 pyrazinamide Not assoc w R
Rv3236c 3612768 p.Ala117Pro missense_variant 0.35 pyrazinamide Uncertain significance
lpqB 3624350 c.561G>T synonymous_variant 0.26 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.17 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3624739 p.Ala58Ser missense_variant 0.41 rifampicin Uncertain significance
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.45 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3841006 p.Asp139His missense_variant 0.34 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.36 pyrazinamide Not assoc w R
glpK 4138377 p.Val460Ala missense_variant 0.18 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
glpK 4139183 c.572dupG frameshift_variant 0.16 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 0.18 ethambutol Not assoc w R
embC 4241843 p.Leu661Ile missense_variant 0.15 ethambutol Not assoc w R
embC 4242550 c.2688C>G synonymous_variant 0.5 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.17 ethambutol Not assoc w R
embA 4244379 p.Pro383Ser missense_variant 0.2 ethambutol Not assoc w R
embA 4245745 p.Pro838Leu missense_variant 0.36 ethambutol Uncertain significance
embB 4246864 c.351C>T synonymous_variant 0.12 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.12 ethambutol Not assoc w R
embB 4248127 c.1614G>A synonymous_variant 0.23 ethambutol Not assoc w R - Interim
aftB 4267232 c.1605C>T synonymous_variant 0.19 ethambutol
aftB 4267272 p.Lys522Arg missense_variant 0.52 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 0.18 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.15 ethambutol Not assoc w R
ubiA 4269522 c.312C>T synonymous_variant 0.18 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.21 ethambutol Not assoc w R
ethA 4326465 p.Ile337Val missense_variant 0.23 ethionamide Uncertain significance
ethA 4326739 c.735C>G synonymous_variant 0.43 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 0.42 ethionamide Not assoc w R - Interim
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 4338673 c.-152G>A upstream_gene_variant 0.32 kanamycin
capreomycin
amikacin
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.17 streptomycin Not assoc w R
gid 4408034 p.Glu57Lys missense_variant 0.17 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.39 streptomycin Not assoc w R