TB-Profiler result

Run: ERR4827935
Summary

Run ID: ERR4827935

Sample name:

Date: 2024-10-05T08:40:37.630003

Number of reads: 4253996

Percentage reads mapped: 99.36

Median coverage: 127.0

Strain: lineage2.2.1;lineage5

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.36
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.4
lineage2.2 East-Asian (Beijing) RD105;RD207 0.3
lineage5 West-Africa 1 RD711 0.48
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
p.Glu761Asp Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Asp354Ala Assoc w R
pyrazinamide
streptomycin rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-37G>T Assoc w R
cycloserine
ethionamide ethA c.-7T>C Assoc w R - Interim
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 0.24 rifampicin Assoc w R
rpoB 762089 p.Glu761Asp missense_variant 0.35 rifampicin Uncertain significance Mutation from literature
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.34 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.31 isoniazid Assoc w R High-level resistance
eis 2715369 c.-37G>T upstream_gene_variant 0.51 kanamycin Assoc w R
embB 4247574 p.Asp354Ala missense_variant 0.38 ethambutol Assoc w R
ethA 4327480 c.-7T>C upstream_gene_variant 0.32 ethionamide Assoc w R - Interim
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 36 c.36G>A synonymous_variant 0.85 isoniazid
gyrB 6446 p.Ala403Ser missense_variant 0.87 levofloxacin Not assoc w R
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 9143 c.1842T>C synonymous_variant 0.86 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
gyrA 9566 c.2265C>T synonymous_variant 0.68 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13460 c.99T>C synonymous_variant 0.7 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 0.43 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.31 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.26 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.2 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.79 ethionamide
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.27 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 0.2 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.43 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253750 p.Asp262Gly missense_variant 0.89 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
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
fbiC 1302899 c.-32A>G upstream_gene_variant 0.53 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
sigE 1364706 c.294G>A synonymous_variant 0.31 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.45 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.66 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.24 pyrazinamide Not assoc w R - Interim
tsnR 1853565 c.-41G>A upstream_gene_variant 0.55 linezolid Uncertain significance
tsnR 1854247 c.642A>G synonymous_variant 0.45 linezolid
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 0.57 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
ndh 2101921 c.1122G>A synonymous_variant 0.67 isoniazid Not assoc w R - Interim
delamanid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155947 c.165T>G synonymous_variant 0.47 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide 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
pncA 2289226 p.Ile6Leu missense_variant 0.33 pyrazinamide Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 0.77 isoniazid
folC 2747433 c.166C>T synonymous_variant 0.8 para-aminosalicylic_acid
pepQ 2860154 c.256_264delCGGGCCGGC conservative_inframe_deletion 0.51 bedaquiline
clofazimine Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 0.45 cycloserine
Rv3083 3449022 c.519C>T synonymous_variant 0.81 ethionamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.24 pyrazinamide Not assoc w R - Interim
lpqB 3624350 c.561G>T synonymous_variant 0.52 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.61 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 0.35 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627920 c.-571A>C upstream_gene_variant 0.54 rifampicin
bedaquiline
alr 3840932 c.489C>T synonymous_variant 0.42 cycloserine
ddn 3986987 c.144G>T synonymous_variant 0.68 pretomanid
delamanid Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.58 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 4139131 p.Glu209Lys missense_variant 0.72 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Not assoc w R
ethambutol Uncertain significance
embC 4239515 c.-348C>T upstream_gene_variant 0.58 ethambutol
embC 4239843 c.-20A>C upstream_gene_variant 0.72 ethambutol Not assoc w R - Interim
embC 4240671 p.Thr270Ile missense_variant 0.52 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 0.4 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.5 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.58 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.45 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.75 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.72 ethambutol Not assoc w R
whiB6 4338563 c.-42G>T upstream_gene_variant 0.44 kanamycin Uncertain significance
capreomycin Not assoc w R
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 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 4407684 p.Glu173Asp missense_variant 0.83 streptomycin
gid 4407927 p.Glu92Asp missense_variant 0.22 streptomycin Not assoc w R