TB-Profiler result

Run: SRR29772466
Summary

Run ID: SRR29772466

Sample name:

Date: 2025-02-11T19:16:23.176054

Number of reads: 3481027

Percentage reads mapped: 99.51

Median coverage: 109.0

Strain: lineage1.1.2;lineage2.2.1.1

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
lineage1.1.2 Indo-Oceanic RD239 0.69
lineage2 East-Asian RD105 0.3
lineage1.1 Indo-Oceanic RD239 0.71
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.3
lineage2.2 East-Asian (Beijing) RD105;RD207 0.3
lineage1 Indo-Oceanic RD239 0.71
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.32
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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val 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
capreomycin
kanamycin
cycloserine
ethionamide ethA p.Pro378Leu Uncertain significance Mutation from literature
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 0.35 levofloxacin Assoc w R
moxifloxacin Assoc w R 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
katG 2155168 p.Ser315Thr missense_variant 0.31 isoniazid Assoc w R High-level resistance
embB 4247429 p.Met306Val missense_variant 0.37 ethambutol Assoc w R
ethA 4326341 p.Pro378Leu missense_variant 0.28 ethionamide Uncertain significance Mutation from literature
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
dnaA 1457 p.Glu486Gly missense_variant 0.7 isoniazid
dnaA 1519 p.Arg507Cys missense_variant 0.78 isoniazid Uncertain significance
gyrB 6112 p.Met291Ile missense_variant 0.68 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.67 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6736 c.1497C>T synonymous_variant 0.6 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 0.64 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.64 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 0.72 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.78 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.32 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.36 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.31 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.28 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.59 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.68 rifampicin Not assoc w R
nusG 734477 p.Val75Gly missense_variant 0.34 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.64 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.64 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.69 rifampicin Not assoc w R
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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.22 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.35 bedaquiline
clofazimine
rpsL 781301 c.-259C>T upstream_gene_variant 0.25 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.72 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406503 p.Val280Leu missense_variant 0.71 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.24 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.68 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.75 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.67 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1473645 n.-12delT upstream_gene_variant 0.73 capreomycin Uncertain significance
linezolid
rpsA 1834177 c.636A>C synonymous_variant 0.24 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.76 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.72 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 0.7 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin 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
Rv1979c 2222308 p.Asp286Gly missense_variant 0.76 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
kasA 2518132 c.18C>T synonymous_variant 0.65 isoniazid
kasA 2518218 p.Gly35Asp missense_variant 0.67 isoniazid
eis 2714846 p.Val163Ile missense_variant 0.29 kanamycin Not assoc w R
amikacin Not assoc w R
ahpC 2726051 c.-142G>A upstream_gene_variant 0.7 isoniazid
folC 2746982 p.Gly206Ala missense_variant 0.32 para-aminosalicylic_acid
Rv2681 2996209 c.-530T>C upstream_gene_variant 0.67 capreomycin
Rv2681 2996912 c.174C>T synonymous_variant 0.68 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.71 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
thyX 3068053 c.-108T>G upstream_gene_variant 0.68 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.77 ethionamide Uncertain significance
Rv3083 3449682 c.1179G>A synonymous_variant 0.72 ethionamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.27 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.7 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.3 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.63 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.62 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 4139183 c.572dupG frameshift_variant 0.2 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 0.77 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.73 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 0.27 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.67 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.74 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.62 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.25 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.39 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.7 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.76 ethambutol Not assoc w R
ethA 4326445 c.1029G>C synonymous_variant 0.68 ethionamide
whiB6 4338224 c.297delC frameshift_variant 0.71 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 0.65 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407732 c.471G>A synonymous_variant 0.36 streptomycin Not assoc w R - Interim
gid 4407873 c.330G>T synonymous_variant 0.68 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.29 streptomycin Not assoc w R