TB-Profiler result

Run: SRR14782033
Summary

Run ID: SRR14782033

Sample name:

Date: 2024-04-15T12:37:22.890382

Number of reads: 2652495

Percentage reads mapped: 99.46

Median coverage: 78.0

Strain: lineage2.2.1;lineage4.8

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.27
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.25
lineage2.2 East-Asian (Beijing) RD105;RD207 0.29
lineage4 Euro-American None 0.71
lineage4.8 Euro-American (mainly T) RD219 0.76
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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
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 0.41 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.39 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.27 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.35 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.28 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.72 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.29 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.24 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.73 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.2 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.22 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 0.31 clofazimine Not assoc w R
bedaquiline Not assoc w R
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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.23 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1304671 p.Val581Leu missense_variant 0.28 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
sigE 1364706 c.294G>A synonymous_variant 0.31 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.26 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 0.87 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.31 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.31 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 0.2 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.22 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.72 pyrazinamide Not assoc w R
PPE35 2168247 p.Leu789Arg missense_variant 0.72 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289952 c.-711C>G upstream_gene_variant 0.73 pyrazinamide
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.81 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.25 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.27 pyrazinamide Not assoc w R - Interim
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.74 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.3 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.26 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878637 c.-130G>C upstream_gene_variant 0.41 rifampicin
rpoA 3878783 c.-276C>T upstream_gene_variant 0.8 rifampicin Uncertain significance
clpC1 4039729 p.Asp326Asn missense_variant 0.75 pyrazinamide Not assoc w R
panD 4043867 p.Gly139* stop_gained 0.27 pyrazinamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.28 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.18 ethambutol Not assoc w R
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 0.27 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.23 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.13 streptomycin Not assoc w R