TB-Profiler result

Run: SRR18715129
Summary

Run ID: SRR18715129

Sample name:

Date: 2024-04-15T03:06:04.337272

Number of reads: 2774398

Percentage reads mapped: 99.28

Median coverage: 84.0

Strain: lineage2.2.1;lineage4.1.2

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 0.25
lineage4.1 Euro-American None 0.73
lineage4.1.2 Euro-American None 0.76
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.24
lineage2.2 East-Asian (Beijing) RD105;RD207 0.28
lineage4 Euro-American None 0.74
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Phe 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
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid ddn p.Trp139* Assoc w R - Interim
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.Ser450Phe missense_variant 0.35 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.25 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.32 isoniazid Assoc w R High-level resistance
ddn 3987259 p.Trp139* stop_gained 0.77 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim
embB 4247429 p.Met306Val missense_variant 0.22 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
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 9037 p.Ala579Val missense_variant 0.78 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.8 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.28 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.25 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.23 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.19 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.22 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.82 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.68 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.2 rifampicin Not assoc w R
rpoC 764116 c.747C>T synonymous_variant 0.8 rifampicin Not assoc w R - Interim
rpoC 764263 c.894G>A synonymous_variant 0.8 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.72 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 0.23 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.27 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 777320 c.1161C>G synonymous_variant 0.73 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mmpR5 779300 p.Glu104Gly missense_variant 0.3 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.33 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800200 c.-609C>G upstream_gene_variant 0.68 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.31 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.33 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471644 n.-202T>C upstream_gene_variant 0.71 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.27 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 0.23 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 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.82 isoniazid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.24 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.15 capreomycin
ald 3086731 c.-89A>G upstream_gene_variant 0.27 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3611974 c.1143A>C synonymous_variant 0.62 pyrazinamide Not assoc w R - Interim
Rv3236c 3612813 p.Thr102Ala missense_variant 0.22 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.28 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.65 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 0.24 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.19 ethambutol Not assoc w R
embB 4247804 p.Ala431Pro missense_variant 0.77 ethambutol Uncertain significance
embB 4249078 c.2565G>A synonymous_variant 0.84 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.18 ethambutol Not assoc w R
whiB6 4338371 p.Thr51Pro missense_variant 0.21 capreomycin Not assoc w R
amikacin Not assoc w R
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 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.2 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.2 streptomycin Not assoc w R