TB-Profiler result

Run: SRR25827695
Summary

Run ID: SRR25827695

Sample name:

Date: 2024-04-16T06:43:43.079011

Number of reads: 2872349

Percentage reads mapped: 49.71

Median coverage: 84.0

Strain: lineage1.1.2;lineage3.1.2

Spoligotype:

Drug-resistance: MDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.24
lineage1.1.2 Indo-Oceanic RD239 0.71
lineage3.1.2 East-African-Indian RD750 0.26
lineage1.1 Indo-Oceanic RD239 0.72
lineage1 Indo-Oceanic RD239 0.74
lineage3.1 East-African-Indian RD750 0.29
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.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C. 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.Gly406Ser Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA c.391dupG Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C
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
rpoB 761155 p.Ser450Leu missense_variant 0.76 rifampicin Assoc w R
inhA 1673432 c.-770T>C upstream_gene_variant 0.79 isoniazid Assoc w R - Interim Alias fabG1_c.-8T>C. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim Alias fabG1_c.-8T>C
katG 2155168 p.Ser315Thr missense_variant 0.2 isoniazid Assoc w R High-level resistance
pncA 2288850 c.391dupG frameshift_variant 0.73 pyrazinamide Assoc w R
embB 4247729 p.Gly406Ser missense_variant 0.72 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.18 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 0.76 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.78 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 0.8 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.77 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 0.79 isoniazid Not assoc w R
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 0.19 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.84 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.72 rifampicin Not assoc w R
nusG 734555 p.Asn101Ser missense_variant 0.77 rifampicin Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.22 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.24 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 0.75 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.76 rifampicin Not assoc w R
rpoC 764666 p.Gly433Cys missense_variant 0.65 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 0.71 rifampicin Not assoc w R
rpoC 765358 p.Met663Ile missense_variant 0.71 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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.76 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
embR 1417019 p.Cys110Tyr missense_variant 0.81 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.77 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.77 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1673405 c.-796delC upstream_gene_variant 0.78 ethionamide Uncertain significance
isoniazid Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.7 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.69 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
tlyA 1918104 c.165G>A synonymous_variant 0.27 capreomycin Not assoc w R - Interim
bacA 2062922 p.Ile603Val missense_variant 0.73 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
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 0.81 pyrazinamide Uncertain significance
PPE35 2168604 p.Pro670Leu missense_variant 0.22 pyrazinamide Not assoc w R
Rv1979c 2222247 c.918C>T synonymous_variant 1.0 clofazimine Not assoc w R - Interim
bedaquiline
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
pncA 2289047 c.195C>T synonymous_variant 0.25 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.22 pyrazinamide
pncA 2290018 c.-777C>T upstream_gene_variant 0.81 pyrazinamide
pncA 2290204 c.-963G>A upstream_gene_variant 0.77 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.74 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.76 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.28 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.22 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 0.7 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.77 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
thyX 3067959 c.-14C>T upstream_gene_variant 0.65 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.7 ethionamide Uncertain significance
whiB7 3568958 c.-279G>A upstream_gene_variant 0.71 streptomycin
amikacin
kanamycin
lpqB 3624486 p.Asp142Gly missense_variant 0.74 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878648 c.-141C>T upstream_gene_variant 0.93 rifampicin Uncertain significance
rpoA 3878875 c.-368C>T upstream_gene_variant 0.82 rifampicin Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.69 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.24 pyrazinamide
panD 4045263 c.-982C>A upstream_gene_variant 0.73 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.77 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 0.36 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 0.73 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.73 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.22 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 0.69 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.79 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.77 ethambutol Not assoc w R
embB 4248320 p.Gly603Arg missense_variant 0.71 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.72 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.73 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 0.76 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 0.73 streptomycin Not assoc w R
gid 4408144 p.Arg20Pro missense_variant 0.75 streptomycin Uncertain significance