TB-Profiler result

Run: SRR25827427
Summary

Run ID: SRR25827427

Sample name:

Date: 2024-10-04T18:36:08.199905

Number of reads: 4822364

Percentage reads mapped: 98.93

Median coverage: 161.0

Strain: lineage1.2.2.2;lineage2.2.1;lineage3;lineage4

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 0.28
lineage1.2.2 Indo-Oceanic RD239 0.34
lineage2 East-Asian RD105 0.25
lineage1.2.2.2 Indo-Oceanic RD239 0.34
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.24
lineage2.2 East-Asian (Beijing) RD105;RD207 0.24
lineage4 Euro-American None 0.08
lineage1 Indo-Oceanic RD239 0.37
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)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Gly132Ala Assoc w R
p.Asp63Gly Assoc w R - Interim
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Gly88Ala Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Gly88Ala Assoc w R - Interim
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
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 7564 p.Gly88Ala missense_variant 0.13 levofloxacin Assoc w R - Interim
moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 0.8 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.35 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.21 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 0.76 isoniazid Assoc w R High-level resistance
pncA 2288847 p.Gly132Ala missense_variant 0.19 pyrazinamide Assoc w R
pncA 2289054 p.Asp63Gly missense_variant 0.14 pyrazinamide Assoc w R - Interim
embB 4247429 p.Met306Val missense_variant 0.16 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.19 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 5052 c.-188A>G upstream_gene_variant 0.2 levofloxacin
moxifloxacin
gyrB 5075 c.-165C>T upstream_gene_variant 0.35 levofloxacin
moxifloxacin
gyrB 5201 c.-39A>G upstream_gene_variant 0.38 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 6112 p.Met291Ile missense_variant 0.34 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 7158 c.1931_1933delCCG disruptive_inframe_deletion 0.37 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7268 c.-34C>T upstream_gene_variant 0.32 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 0.91 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.34 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.36 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.96 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.32 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.22 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.34 isoniazid Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.2 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.94 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.2 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.19 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.5 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.15 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.41 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.37 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.28 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.29 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.89 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.46 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.45 rifampicin Not assoc w R
rpoC 764840 p.Ile491Val missense_variant 0.16 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.93 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.18 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.22 bedaquiline
clofazimine
rpsL 781241 c.-319C>T upstream_gene_variant 0.37 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781879 p.Val107Ala missense_variant 0.22 streptomycin Uncertain significance
rplC 800233 c.-576G>A upstream_gene_variant 0.28 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.31 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406170 p.Gly391Arg missense_variant 0.44 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.23 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.35 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.35 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.4 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471754 n.-92T>G upstream_gene_variant 0.38 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.38 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.88 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 0.48 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
ndh 2101756 c.1287G>T synonymous_variant 0.41 isoniazid
delamanid
ethionamide
katG 2154724 p.Arg463Leu missense_variant 0.9 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.93 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.37 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.45 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
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.37 bedaquiline Uncertain significance
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.23 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.29 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.34 isoniazid
eis 2714177 p.Leu386Ile missense_variant 0.31 kanamycin Uncertain significance
amikacin Uncertain significance
ahpC 2726051 c.-142G>A upstream_gene_variant 0.49 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.28 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.31 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2680 2996207 p.Ala35Thr missense_variant 0.21 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.95 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.41 ethionamide Uncertain significance
Rv3236c 3612563 p.Met185Thr missense_variant 0.24 pyrazinamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.2 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.37 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.92 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626467 c.147G>A synonymous_variant 0.39 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.2 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.39 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.33 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.43 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 4138622 c.1134C>T synonymous_variant 0.33 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.37 ethambutol Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.17 ethambutol Uncertain significance
embC 4241042 p.Asn394Asp missense_variant 0.37 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.3 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 0.15 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.41 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.26 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.33 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.27 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.41 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.44 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.31 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.29 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.33 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338533 c.-12T>C upstream_gene_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 4338603 c.-82C>T upstream_gene_variant 0.46 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.92 kanamycin
capreomycin
amikacin
whiB6 4338841 c.-320G>A upstream_gene_variant 0.22 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.93 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.18 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.41 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.2 streptomycin Not assoc w R