TB-Profiler result

Run: ERR133972
Summary

Run ID: ERR133972

Sample name:

Date: 2024-04-15T18:19:08.867021

Number of reads: 9717674

Percentage reads mapped: 99.62

Median coverage: 212.0

Strain: lineage2.2.1;lineage4.8

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 0.51
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.5
lineage2.2 East-Asian (Beijing) RD105;RD207 0.5
lineage4 Euro-American None 0.53
lineage4.8 Euro-American (mainly T) RD219 0.51
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 rpsL p.Lys88Arg Assoc w R
rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
c.-37G>T Assoc w R
cycloserine
ethionamide ethA c.754_755dupGC Assoc w R
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 0.99 rifampicin Assoc w R
rpoB 762089 p.Glu761Asp missense_variant 0.52 rifampicin Uncertain significance Mutation from literature
rpsL 781822 p.Lys88Arg missense_variant 0.49 streptomycin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.5 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.51 isoniazid Assoc w R High-level resistance
eis 2715342 c.-10G>A upstream_gene_variant 0.49 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
eis 2715369 c.-37G>T upstream_gene_variant 0.51 kanamycin Assoc w R
embB 4247574 p.Asp354Ala missense_variant 0.5 ethambutol Assoc w R
ethA 4326718 c.754_755dupGC frameshift_variant 0.45 ethionamide Assoc w R
ethA 4327480 c.-7T>C upstream_gene_variant 0.51 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
gyrB 6432 p.Ala398Val 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 0.43 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.52 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.55 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.5 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.55 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.44 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.44 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.57 rifampicin Not assoc w R
rpoC 764916 p.Leu516Pro missense_variant 0.48 rifampicin Uncertain significance
rpoC 766645 p.Glu1092Asp missense_variant 0.47 rifampicin Not assoc w R
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 0.5 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.51 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.46 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.48 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.5 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.42 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.54 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.53 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.56 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.49 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.55 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.53 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289226 p.Ile6Leu missense_variant 0.55 pyrazinamide Not assoc w R - Interim
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.57 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.52 cycloserine
Rv3083 3448383 c.-121T>C upstream_gene_variant 0.5 ethionamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.43 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.49 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.52 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3642793 p.Pro420Leu missense_variant 0.47 clofazimine
pretomanid
delamanid
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.48 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.43 ethambutol Not assoc w R
whiB6 4338563 c.-42G>T upstream_gene_variant 0.5 capreomycin Not assoc w R
amikacin Uncertain significance
kanamycin Uncertain significance
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 4338732 c.-211C>T upstream_gene_variant 0.51 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.52 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.5 streptomycin Not assoc w R