TB-Profiler result

Run: SRR25827441
Summary

Run ID: SRR25827441

Sample name:

Date: 2024-04-15T23:23:06.019780

Number of reads: 9246542

Percentage reads mapped: 98.0

Median coverage: 305.0

Strain: lineage1.1.2;lineage2.2.1;lineage3.1.2

Spoligotype:

Drug-resistance: HR-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 0.43
lineage1.1.2 Indo-Oceanic RD239 0.42
lineage3.1.2 East-African-Indian RD750 0.38
lineage2 East-Asian RD105 0.09
lineage1.1 Indo-Oceanic RD239 0.43
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.11
lineage2.2 East-Asian (Beijing) RD105;RD207 0.09
lineage1 Indo-Oceanic RD239 0.41
lineage3.1 East-African-Indian RD750 0.43
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
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)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly 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
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 7582 p.Asp94Gly missense_variant 0.16 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.17 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.18 amikacin Assoc w R
kanamycin Assoc w R
capreomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.54 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)
katG 2155168 p.Ser315Thr missense_variant 0.14 isoniazid Assoc w R High-level resistance
embB 4248003 p.Gln497Arg missense_variant 0.15 ethambutol 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 6112 p.Met291Ile missense_variant 0.41 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.42 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6372 p.Thr378Ser missense_variant 0.47 levofloxacin Uncertain significance
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 8452 p.Ala384Val missense_variant 0.45 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.39 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 0.49 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.3 isoniazid Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.23 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
Rv0565c 657081 c.390G>A synonymous_variant 0.63 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.21 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.45 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.41 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.42 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.48 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.41 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.47 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 0.41 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.4 rifampicin Not assoc w R
rpoC 764840 p.Ile491Val missense_variant 0.17 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 0.37 rifampicin Not assoc w R
rpoC 767134 c.3765C>T synonymous_variant 0.39 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 776182 p.Asp767Asn missense_variant 0.17 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 776395 p.Phe696Leu missense_variant 0.36 clofazimine Not assoc w R
bedaquiline Uncertain significance
mmpL5 777119 c.1362C>T synonymous_variant 0.41 clofazimine
bedaquiline
mmpS5 779615 c.-710C>G upstream_gene_variant 0.15 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 0.42 linezolid 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
fbiC 1303928 p.Ala333Val missense_variant 0.44 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.39 ethambutol Not assoc w R
embR 1417249 c.99C>A synonymous_variant 0.46 ethambutol Not assoc w R - Interim
embR 1417330 c.18A>C synonymous_variant 0.41 ethambutol Not assoc w R - Interim
embR 1417554 c.-207C>G upstream_gene_variant 0.43 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.45 ethambutol
rrs 1471522 n.-324T>G upstream_gene_variant 0.46 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834972 c.1431C>T synonymous_variant 0.36 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.41 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.46 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 0.38 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2103053 c.-11A>G upstream_gene_variant 0.17 ethionamide
delamanid
isoniazid
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 2167983 p.Gly877Asp missense_variant 0.39 pyrazinamide Uncertain significance
PPE35 2168604 p.Pro670Leu missense_variant 0.41 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.39 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
pncA 2289047 c.195C>T synonymous_variant 0.46 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.44 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.47 isoniazid
eis 2714672 p.Asp221Asn missense_variant 0.41 amikacin
kanamycin
ahpC 2726051 c.-142G>A upstream_gene_variant 0.46 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.41 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.38 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
Rv2681 2996912 c.174C>T synonymous_variant 0.47 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.45 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 0.44 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.17 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.4 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 3626346 p.Gly90Arg missense_variant 0.4 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3626467 c.147G>A synonymous_variant 0.43 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.46 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.41 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.51 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.37 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 0.41 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 0.42 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.43 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.51 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 0.46 ethambutol Not assoc w R
embA 4245218 c.1986C>T synonymous_variant 0.43 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.46 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.4 ethambutol Not assoc w R
ubiA 4269031 p.Gly268Asp missense_variant 0.42 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.45 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.48 ethambutol 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 0.42 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
whiB6 4338881 c.-360G>A upstream_gene_variant 0.44 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407861 c.342C>A synonymous_variant 0.43 streptomycin
gid 4407873 c.330G>T synonymous_variant 0.45 streptomycin Not assoc w R
gid 4407902 p.Leu101Phe missense_variant 0.47 streptomycin Uncertain significance