TB-Profiler result

Run: SRR15369025
Summary

Run ID: SRR15369025

Sample name:

Date: 2024-10-05T10:21:50.653060

Number of reads: 6615375

Percentage reads mapped: 99.41

Median coverage: 196.0

Strain: lineage2.2.2;lineage4.4.2

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 0.81
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.8
lineage2.2 East-Asian (Beijing) RD105;RD207 0.83
lineage4 Euro-American None 0.18
lineage4.4 Euro-American None 0.14
lineage4.4.2 Euro-American None 0.13
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 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 491742 c.960T>C synonymous_variant 0.78 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.81 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.8 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.83 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 0.83 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.79 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781406 c.-154_-153insC upstream_gene_variant 0.77 streptomycin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.83 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
sigE 1364671 c.259C>T synonymous_variant 0.82 pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1833909 p.Asp123Ala missense_variant 0.81 pyrazinamide Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.81 pyrazinamide Not assoc w R - Interim
tsnR 1853577 c.-29G>A upstream_gene_variant 0.15 linezolid Uncertain significance
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 0.84 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.8 pyrazinamide Not assoc w R
PPE35 2168757 p.Gln619Arg missense_variant 0.16 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2752c 3066099 p.Met31Ile missense_variant 0.15 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.14 ethionamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.86 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627655 c.-306G>T upstream_gene_variant 0.82 rifampicin
bedaquiline
clpC1 4040857 c.-153C>T upstream_gene_variant 0.85 pyrazinamide
panD 4044920 c.-639C>T upstream_gene_variant 0.85 pyrazinamide
embC 4238963 c.-900C>T upstream_gene_variant 0.14 ethambutol 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 0.85 ethambutol Not assoc w R
embA 4244365 p.Gly378Ala missense_variant 0.86 ethambutol
embA 4246508 c.3276G>A synonymous_variant 0.15 ethambutol Not assoc w R
embB 4247249 p.Gly246Arg missense_variant 0.13 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.76 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 0.2 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.14 ethambutol Not assoc w R
ethA 4327531 c.-58T>C upstream_gene_variant 0.78 ethionamide
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
whiB6 4338733 c.-212T>C upstream_gene_variant 0.77 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.8 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.77 streptomycin Not assoc w R
gid 4408090 p.Pro38Arg missense_variant 0.17 streptomycin