TB-Profiler result

Run: SRR20969477
Summary

Run ID: SRR20969477

Sample name:

Date: 2024-10-04T10:46:49.209902

Number of reads: 10375388

Percentage reads mapped: 99.62

Median coverage: 282.5

Strain: lineage2.2.1;lineage4.4.2

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.71
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.71
lineage2.2 East-Asian (Beijing) RD105;RD207 0.74
lineage4 Euro-American None 0.29
lineage4.4 Euro-American None 0.28
lineage4.4.2 Euro-American None 0.28
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
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.1047delT Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 0.26 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.32 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.26 isoniazid Assoc w R High-level resistance
embB 4248003 p.Gln497Arg missense_variant 0.21 ethambutol Assoc w R
ethA 4326426 c.1047delT frameshift_variant 0.25 ethionamide 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.69 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.69 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 576164 p.Arg273Cys missense_variant 0.29 isoniazid
ethionamide
ccsA 620625 p.Ile245Met missense_variant 0.71 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.69 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.69 ethionamide Uncertain significance
Rv0565c 657371 p.Gln34* stop_gained 0.27 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.67 rifampicin Not assoc w R
rpoC 766992 p.Met1208Thr missense_variant 0.32 rifampicin Uncertain significance
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 0.74 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.76 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.74 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.72 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472986 n.1141C>T non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
inhA 1674090 c.-112C>T upstream_gene_variant 0.25 isoniazid Uncertain significance
ethionamide Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.75 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 0.68 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.64 pyrazinamide Not assoc w R
PPE35 2170849 c.-237T>A upstream_gene_variant 0.32 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289559 c.-318T>G upstream_gene_variant 0.71 pyrazinamide
Rv2752c 3065256 p.Met312Ile missense_variant 0.29 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3066099 p.Met31Ile missense_variant 0.25 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 1.0 cycloserine
Rv3236c 3612608 p.Ala170Val missense_variant 0.23 pyrazinamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.72 pyrazinamide 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 0.74 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4238963 c.-900C>T upstream_gene_variant 0.33 ethambutol Not assoc w R
embC 4242241 c.2379C>T synonymous_variant 0.7 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.7 ethambutol Not assoc w R
embA 4246508 c.3276G>A synonymous_variant 0.28 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.73 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 0.27 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.26 ethambutol Not assoc w R
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 0.73 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.75 streptomycin Not assoc w R