TB-Profiler result

Run: SRR25827875
Summary

Run ID: SRR25827875

Sample name:

Date: 2024-04-15T03:54:34.356809

Number of reads: 8393187

Percentage reads mapped: 99.25

Median coverage: 286.0

Strain: lineage1.2.2.2;lineage2.2.1;lineage3

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.37
lineage1.2.2 Indo-Oceanic RD239 0.18
lineage2 East-Asian RD105 0.43
lineage1.2.2.2 Indo-Oceanic RD239 0.17
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.45
lineage2.2 East-Asian (Beijing) RD105;RD207 0.43
lineage1 Indo-Oceanic RD239 0.18
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Ile194Thr Uncertain significance Mutation from literature
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gly406Ser Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Arg154Gly Assoc w R
p.Gly132Ala Assoc w R
p.Leu27Pro Assoc w R
p.Asp12Glu Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine ald c.436_437dupGC Mutation from literature
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
p.Ile194Thr Uncertain significance Mutation from literature
ethA c.1152dupT Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 0.15 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.32 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.41 kanamycin Assoc w R
amikacin Assoc w R
capreomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.35 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
inhA 1674782 p.Ile194Thr missense_variant 0.21 isoniazid Uncertain significance Mutation from literature
ethionamide Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.84 isoniazid Assoc w R High-level resistance
pncA 2288782 p.Arg154Gly missense_variant 0.2 pyrazinamide Assoc w R
pncA 2288847 p.Gly132Ala missense_variant 0.24 pyrazinamide Assoc w R
pncA 2289162 p.Leu27Pro missense_variant 0.18 pyrazinamide Assoc w R
pncA 2289206 p.Asp12Glu missense_variant 0.43 pyrazinamide Assoc w R
ald 3087252 c.436_437dupGC frameshift_variant 0.14 cycloserine Mutation from literature
embB 4247729 p.Gly406Ser missense_variant 0.23 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.25 ethambutol Assoc w R
ethA 4326321 c.1152dupT frameshift_variant 0.36 ethionamide 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
gyrB 5075 c.-165C>T upstream_gene_variant 0.21 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.14 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 7581 p.Asp94Cys missense_variant 0.25 levofloxacin
moxifloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.14 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 13298 p.Ile87Met missense_variant 0.15 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.17 isoniazid Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.22 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.17 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.46 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.81 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.39 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.23 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.14 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.38 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.43 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.17 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.16 rifampicin Not assoc w R
rpoC 764840 p.Ile491Val missense_variant 0.13 rifampicin Uncertain significance
rpoC 765060 p.Asn564Ser missense_variant 0.17 rifampicin
rpoC 766466 p.Glu1033Lys missense_variant 0.37 rifampicin Uncertain significance
rpoC 766488 p.Pro1040Arg missense_variant 0.19 rifampicin Uncertain significance
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 776182 p.Asp767Asn missense_variant 0.22 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.44 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.15 linezolid Not assoc w R
Rv1129c 1253177 p.Thr453Met missense_variant 0.36 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
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
Rv1258c 1406760 c.580_581insC frameshift_variant 0.45 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.16 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.13 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.2 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471869 n.24G>A non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473368 n.1523G>A non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.43 pyrazinamide Not assoc w R - Interim
rpsA 1834940 p.Asp467Asn missense_variant 0.15 pyrazinamide
tsnR 1853974 c.369C>T synonymous_variant 0.19 linezolid Not assoc w R
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 0.21 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2101727 p.Arg439Leu missense_variant 0.15 ethionamide
delamanid
isoniazid
ndh 2102240 p.Arg268His missense_variant 0.17 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R - Interim
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
PPE35 2168742 p.Gly624Asp missense_variant 0.17 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.19 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2222700 c.465C>T synonymous_variant 0.38 clofazimine Not assoc w R - Interim
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
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.19 clofazimine Not assoc w R
bedaquiline Uncertain significance
pncA 2289047 c.195C>T synonymous_variant 0.44 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.4 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.15 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.14 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.37 isoniazid Not assoc w R
folC 2747453 p.Arg49Gln missense_variant 0.22 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.36 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2477c 2784204 c.-162A>C upstream_gene_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2680 2996651 p.Val183Phe missense_variant 0.21 capreomycin Uncertain significance
Rv2752c 3064700 p.Ser498Pro missense_variant 0.16 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087601 p.Gly261Val missense_variant 0.2 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.14 ethionamide Uncertain significance
whiB7 3568428 c.252A>C synonymous_variant 0.14 streptomycin
amikacin
kanamycin
whiB7 3568893 c.-215delC upstream_gene_variant 0.18 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB7 3569039 c.-360T>G upstream_gene_variant 0.2 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin
whiB7 3569220 c.-541C>T upstream_gene_variant 0.18 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.43 pyrazinamide Not assoc w R - Interim
lpqB 3623174 c.1737G>C synonymous_variant 0.38 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.15 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.16 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.43 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841473 c.-53G>A upstream_gene_variant 0.42 cycloserine
clpC1 4040517 p.Val63Ala missense_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4040719 c.-15A>G upstream_gene_variant 0.19 pyrazinamide Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.38 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.16 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 4138622 c.1134C>T synonymous_variant 0.35 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.18 ethambutol Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.14 ethambutol Uncertain significance
embC 4241042 p.Asn394Asp missense_variant 0.18 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.39 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.5 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.19 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.2 ethambutol
embB 4247429 c.916_918delATGinsGA frameshift_variant&missense_variant 0.23 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.2 ethambutol Not assoc w R
aftB 4267492 p.Ala449Thr missense_variant 0.36 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.43 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.15 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.21 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.16 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.19 ethionamide Uncertain significance
ethA 4326676 p.Ser266Arg missense_variant 0.24 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.24 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
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 0.18 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 0.99 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.18 streptomycin Not assoc w R
gid 4407790 p.Ala138Glu missense_variant 0.2 streptomycin Uncertain significance
gid 4407848 p.Ala119Thr missense_variant 0.18 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.2 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.39 streptomycin Not assoc w R
gid 4407967 p.Leu79Trp missense_variant 0.4 streptomycin Uncertain significance