TB-Profiler result

Run: SRR26399491
Summary

Run ID: SRR26399491

Sample name:

Date: 2024-04-15T18:12:27.119086

Number of reads: 1335079

Percentage reads mapped: 98.49

Median coverage: 36.0

Strain: lineage1.1.1.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1 Indo-Oceanic RD239 1.0
lineage1 Indo-Oceanic RD239 1.0
lineage1.1.1 Indo-Oceanic RD239 0.98
lineage1.1.1.1 Indo-Oceanic RD239 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
gyrB 6112 p.Met291Ile missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 8452 p.Ala384Val missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_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
Rv0010c 13275 p.Tyr95Cys missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 1.0 isoniazid Not assoc w R
fgd1 490972 p.Arg64Ser missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.97 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657542 c.-72G>A upstream_gene_variant 1.0 ethionamide
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoC 762383 c.-987C>A upstream_gene_variant 0.16 rifampicin
rpoC 762398 c.-972T>G upstream_gene_variant 0.15 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 1.0 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764746 c.1377G>A synonymous_variant 0.28 rifampicin
rpoC 764752 c.1383G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764758 c.1389C>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 764791 c.1422C>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.31 rifampicin Not assoc w R
rpoC 764812 c.1443C>G synonymous_variant 0.31 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764824 c.1455T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 764875 c.1506C>G synonymous_variant 0.33 rifampicin
rpoC 764878 c.1509C>T synonymous_variant 0.33 rifampicin
rpoC 764888 c.1519T>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764893 c.1524T>C synonymous_variant 0.34 rifampicin
rpoC 764911 c.1542A>G synonymous_variant 0.33 rifampicin
rpoC 764953 c.1584G>C synonymous_variant 0.34 rifampicin
rpoC 764968 c.1599T>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 765171 p.Pro601Leu missense_variant 0.98 rifampicin Not assoc w R
rpoC 766765 c.3396A>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.34 rifampicin
rpoC 766777 c.3408C>G synonymous_variant 0.33 rifampicin
rpoC 766798 c.3429C>G synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 766801 c.3432C>G synonymous_variant 0.33 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 766861 c.3492G>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.38 rifampicin
rpoC 766894 c.3525T>C synonymous_variant 0.39 rifampicin
rpoC 766895 c.3526T>C synonymous_variant 0.4 rifampicin
rpoC 766900 c.3531T>C synonymous_variant 0.38 rifampicin
rpoC 766918 c.3549C>T synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoC 766933 c.3564A>G synonymous_variant 0.4 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.33 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 767059 c.3690T>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.3 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
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 777581 p.Tyr300* stop_gained 0.97 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.96 linezolid Not assoc w R
Rv1129c 1254543 c.-9T>G upstream_gene_variant 1.0 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
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
embR 1417019 p.Cys110Tyr missense_variant 1.0 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833742 c.201A>G synonymous_variant 0.31 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.31 pyrazinamide
rpsA 1833802 c.261A>G synonymous_variant 0.31 pyrazinamide
rpsA 1833811 c.270G>T synonymous_variant 0.38 pyrazinamide
rpsA 1833820 c.279G>A synonymous_variant 0.31 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.28 pyrazinamide
rpsA 1833859 c.318C>T synonymous_variant 0.3 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.27 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.29 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.28 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.24 pyrazinamide
rpsA 1833976 c.435C>T synonymous_variant 0.19 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.2 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.21 pyrazinamide
rpsA 1834319 p.Val260Ile missense_variant 0.87 pyrazinamide Uncertain significance
rpsA 1834546 c.1005T>C synonymous_variant 0.3 pyrazinamide
rpsA 1834600 c.1059G>C synonymous_variant 0.28 pyrazinamide
rpsA 1834606 c.1065C>T synonymous_variant 0.27 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.28 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.26 pyrazinamide
tsnR 1853974 c.369C>T synonymous_variant 1.0 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 1.0 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tsnR 1854310 c.705A>C synonymous_variant 0.98 linezolid Not assoc w R - Interim
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.97 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063106 c.1623G>A synonymous_variant 0.98 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2156389 c.-278G>C upstream_gene_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.97 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.96 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 1.0 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3625183 c.-273G>C upstream_gene_variant 0.17 bedaquiline
rifampicin
lpqB 3625186 c.-276T>G upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrB 3625189 c.1425A>G synonymous_variant 0.16 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625195 c.-285A>C upstream_gene_variant 0.17 bedaquiline
rifampicin
lpqB 3625198 c.-288C>G upstream_gene_variant 0.16 bedaquiline
rifampicin
lpqB 3625201 c.-291T>C upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrB 3625222 c.1392T>C synonymous_variant 0.2 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625240 c.-330T>C upstream_gene_variant 0.25 bedaquiline
rifampicin
lpqB 3625243 c.-333T>C upstream_gene_variant 0.25 bedaquiline
rifampicin
lpqB 3625246 c.-336G>A upstream_gene_variant 0.27 bedaquiline
rifampicin
lpqB 3625255 c.-345T>C upstream_gene_variant 0.28 bedaquiline
rifampicin
lpqB 3625258 c.-348G>C upstream_gene_variant 0.28 bedaquiline
rifampicin
mtrB 3625267 c.1347T>C synonymous_variant 0.32 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625270 c.-360G>C upstream_gene_variant 0.3 bedaquiline
rifampicin
lpqB 3625282 c.-372C>G upstream_gene_variant 0.31 bedaquiline
rifampicin
mtrB 3625747 c.867G>C synonymous_variant 0.13 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625993 c.621G>C synonymous_variant 0.14 bedaquiline
rifampicin
mtrB 3626705 c.-92G>T upstream_gene_variant 0.22 bedaquiline
rifampicin
mtrB 3626711 c.-98T>C upstream_gene_variant 0.21 bedaquiline
rifampicin
mtrA 3626723 c.627C>T synonymous_variant 0.32 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626744 c.-131G>C upstream_gene_variant 0.4 bedaquiline
rifampicin
mtrB 3626750 c.-137T>C upstream_gene_variant 0.42 bedaquiline
rifampicin
mtrA 3626759 c.591T>C synonymous_variant 0.41 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626774 c.574_576delAGGinsCT frameshift_variant&missense_variant 0.43 bedaquiline
rifampicin
mtrB 3626780 c.-167T>C upstream_gene_variant 0.44 bedaquiline
rifampicin
mtrB 3626783 c.-170C>G upstream_gene_variant 0.44 bedaquiline
rifampicin
mtrA 3626786 c.564A>G synonymous_variant 0.44 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626798 c.-185T>C upstream_gene_variant 0.45 bedaquiline
rifampicin
mtrB 3626804 c.-191A>C upstream_gene_variant 0.48 bedaquiline
rifampicin
mtrB 3626843 c.-230G>C upstream_gene_variant 0.47 bedaquiline
rifampicin
mtrA 3626846 c.504G>A synonymous_variant 0.44 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626849 c.-236C>T upstream_gene_variant 0.49 bedaquiline
rifampicin
mtrB 3626858 c.-245A>G upstream_gene_variant 0.48 bedaquiline
rifampicin
mtrB 3626866 c.-253T>C upstream_gene_variant 0.46 bedaquiline
rifampicin
mtrB 3626885 c.-272A>G upstream_gene_variant 0.44 bedaquiline
rifampicin
mtrB 3626890 c.-277T>C upstream_gene_variant 0.42 bedaquiline
rifampicin
mtrA 3626912 c.438T>C synonymous_variant 0.45 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626930 c.-317A>G upstream_gene_variant 0.45 bedaquiline
rifampicin
mtrA 3626939 p.Glu137Asp missense_variant 0.44 bedaquiline
rifampicin
mtrB 3626942 c.-329A>C upstream_gene_variant 0.43 bedaquiline
rifampicin
fbiB 3642535 p.Arg334Gln missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
clpC1 4039073 c.1632C>G synonymous_variant 0.24 pyrazinamide
clpC1 4039079 c.1626C>G synonymous_variant 0.23 pyrazinamide Not assoc w R - Interim
clpC1 4039082 c.1623C>T synonymous_variant 0.22 pyrazinamide
clpC1 4039085 c.1620A>G synonymous_variant 0.24 pyrazinamide
clpC1 4039097 c.1608G>T synonymous_variant 0.27 pyrazinamide
clpC1 4039106 c.1599G>C synonymous_variant 0.27 pyrazinamide
clpC1 4039112 c.1593C>G synonymous_variant 0.25 pyrazinamide
clpC1 4039121 c.1584T>C synonymous_variant 0.24 pyrazinamide
clpC1 4039136 c.1569C>T synonymous_variant 0.25 pyrazinamide
clpC1 4039140 p.Glu522Val missense_variant 0.23 pyrazinamide
clpC1 4039142 c.1563A>G synonymous_variant 0.22 pyrazinamide
clpC1 4039145 c.1560G>C synonymous_variant 0.22 pyrazinamide
clpC1 4040200 c.505T>C synonymous_variant 0.2 pyrazinamide
clpC1 4040201 c.504C>G synonymous_variant 0.17 pyrazinamide
clpC1 4040204 c.501G>C synonymous_variant 0.17 pyrazinamide
clpC1 4040207 c.498T>C synonymous_variant 0.18 pyrazinamide
clpC1 4040213 c.490_492delTCTinsAGC synonymous_variant 0.17 pyrazinamide
clpC1 4040225 c.480A>C synonymous_variant 0.18 pyrazinamide
clpC1 4040228 c.477G>A synonymous_variant 0.18 pyrazinamide
clpC1 4040231 c.474C>G synonymous_variant 0.2 pyrazinamide
clpC1 4040237 c.468C>T synonymous_variant 0.2 pyrazinamide
clpC1 4040249 c.456A>G synonymous_variant 0.19 pyrazinamide
clpC1 4040258 c.447G>A synonymous_variant 0.19 pyrazinamide
clpC1 4040267 c.438A>G synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4040277 c.427_428delTCinsAG synonymous_variant 0.16 pyrazinamide
clpC1 4040279 c.426C>G synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4040300 c.405C>T synonymous_variant 0.17 pyrazinamide
clpC1 4040306 c.399G>C synonymous_variant 0.23 pyrazinamide
clpC1 4040315 c.390G>A synonymous_variant 0.2 pyrazinamide
clpC1 4040321 c.384C>T synonymous_variant 0.19 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 0.96 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4139074 p.Leu228Val missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 1.0 ethambutol Not assoc w R
embA 4244096 c.864C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 1.0 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_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 4338242 p.Gln94Glu missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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 4338603 c.-82C>T 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 4407873 c.330G>T synonymous_variant 1.0 streptomycin Not assoc w R