TB-Profiler result

Run: ERR11773836
Summary

Run ID: ERR11773836

Sample name:

Date: 2024-10-04T18:41:35.488044

Number of reads: 4341525

Percentage reads mapped: 99.6

Median coverage: 130.0

Strain: lineage2.2.1;lineage4.1.2.1

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 0.2
lineage4.1 Euro-American None 0.83
lineage4.1.2 Euro-American None 0.82
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.83
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.18
lineage2.2 East-Asian (Beijing) RD105;RD207 0.19
lineage4 Euro-American None 0.81
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 0.25 rifampicin Assoc w R
rpoB 762089 p.Glu761Asp missense_variant 0.16 rifampicin Uncertain significance Mutation from literature
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.15 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.15 isoniazid Assoc w R High-level resistance
eis 2715369 c.-37G>T upstream_gene_variant 0.22 kanamycin Assoc w R
embB 4247574 p.Asp354Ala missense_variant 0.15 ethambutol Assoc w R
ethA 4327480 c.-7T>C upstream_gene_variant 0.25 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 6000 p.Pro254Leu missense_variant 0.79 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 1.0 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
fgd1 491591 p.Lys270Met missense_variant 0.89 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.16 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.83 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.17 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 0.21 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.19 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.87 ethionamide Uncertain significance
rpoB 760106 c.300G>A synonymous_variant 0.89 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.88 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.22 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.84 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.2 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 0.25 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 0.2 bedaquiline
clofazimine
rpsL 781276 c.-284A>C upstream_gene_variant 0.87 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.15 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254583 c.-49A>C upstream_gene_variant 0.86 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.22 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
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
katG 2154724 p.Arg463Leu missense_variant 0.13 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.21 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
kasA 2518076 c.-39C>T upstream_gene_variant 0.78 isoniazid
Rv2680 2996136 p.Ser11Asn missense_variant 0.16 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.13 pyrazinamide Not assoc w R - Interim
lpqB 3624227 c.684G>A synonymous_variant 0.75 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.23 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.83 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.85 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.2 ethambutol Not assoc w R
embB 4247284 c.771G>C synonymous_variant 0.84 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.18 ethambutol Not assoc w R
whiB6 4338513 c.9C>T synonymous_variant 0.88 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
whiB6 4338563 c.-42G>T upstream_gene_variant 0.16 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 0.21 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.16 streptomycin Not assoc w R
gid 4408102 p.Gly34Glu missense_variant 0.8 streptomycin Uncertain significance