TB-Profiler result

Run: SRR10315458
Summary

Run ID: SRR10315458

Sample name:

Date: 2024-04-16T10:27:08.665375

Number of reads: 6127289

Percentage reads mapped: 99.64

Median coverage: 159.0

Strain: lineage2.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.22
lineage2 East-Asian RD105 0.76
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.79
lineage2.2 East-Asian (Beijing) RD105;RD207 0.8
lineage4 Euro-American None 0.21
lineage4.3.3 Euro-American (LAM) RD115 0.22
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu430Pro Assoc w R
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ahpC c.-52C>T Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
p.Gly406Ala Assoc w R
pyrazinamide
streptomycin rrs n.908A>G Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.-11A>G 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
rpoB 761095 p.Leu430Pro missense_variant 0.81 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.19 rifampicin Assoc w R
rrs 1472753 n.908A>G non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.18 isoniazid Assoc w R High-level resistance
ahpC 2726141 c.-52C>T upstream_gene_variant 0.12 isoniazid Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.18 ethambutol Assoc w R
embB 4247730 p.Gly406Ala missense_variant 0.19 ethambutol Assoc w R
ethA 4327484 c.-11A>G upstream_gene_variant 0.27 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
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 8040 p.Gly247Ser missense_variant 0.17 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 491556 c.774G>A synonymous_variant 0.82 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.86 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.74 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.74 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.77 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.79 ethionamide Uncertain significance
rpoB 761547 p.Val581Met missense_variant 0.2 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.81 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.2 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 0.82 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.81 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.79 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 0.87 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 0.68 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.22 capreomycin Not assoc w R
linezolid Uncertain significance
inhA 1674210 c.9A>C synonymous_variant 0.81 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.75 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.99 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 0.78 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.84 pyrazinamide Not assoc w R
Rv1979c 2223051 p.Glu38Asp missense_variant 0.17 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 0.21 isoniazid
Rv2752c 3064519 c.1672delG frameshift_variant 0.75 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv2752c 3065824 p.Pro123Leu missense_variant 0.18 ethambutol Not assoc w R
moxifloxacin Uncertain significance
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 0.14 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.78 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 0.74 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038169 p.Ala846Pro missense_variant 0.82 pyrazinamide
clpC1 4038287 c.2418C>T synonymous_variant 0.19 pyrazinamide 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 0.77 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.76 ethambutol Not assoc w R
whiB6 4338286 p.Val79Ala missense_variant 0.79 capreomycin Uncertain significance
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 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.84 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.19 streptomycin Not assoc w R