TB-Profiler result

Run: SRR13837486
Summary

Run ID: SRR13837486

Sample name:

Date: 2024-04-16T03:24:33.232955

Number of reads: 883475

Percentage reads mapped: 98.22

Median coverage: 30.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 1.0
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
dnaA 497 p.Thr166Ser missense_variant 1.0 isoniazid
dnaA 558 c.558G>T synonymous_variant 1.0 isoniazid
gyrB 5333 p.Met32Val missense_variant 1.0 levofloxacin
moxifloxacin
ccsA 620509 p.Thr207Ser missense_variant 1.0 capreomycin
amikacin
kanamycin
ccsA 620749 p.Trp287Arg missense_variant 1.0 capreomycin
amikacin
kanamycin
rpoC 766954 c.3586delG frameshift_variant 1.0 rifampicin
mmpL5 776080 p.Ala801Pro missense_variant 1.0 clofazimine
bedaquiline
rplC 801220 p.Ser138Gly missense_variant 1.0 linezolid
fbiC 1303494 p.Leu188Phe missense_variant 1.0 clofazimine
pretomanid
delamanid
rrl 1476502 n.2845G>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
fabG1 1673622 p.Asp61Glu missense_variant 1.0 ethionamide
isoniazid
fabG1 1673718 c.279_280insT frameshift_variant&stop_gained 1.0 ethionamide
isoniazid
katG 2155998 p.Trp38Cys missense_variant 1.0 isoniazid
katG 2156285 c.-174T>G upstream_gene_variant 1.0 isoniazid
ahpC 2726085 c.-108G>A upstream_gene_variant 0.96 isoniazid
Rv2477c 2782501 c.1542T>C synonymous_variant 1.0 ethambutol
moxifloxacin Not assoc w R - Interim
streptomycin
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ribD 2987458 p.Val207Ala missense_variant 1.0 para-aminosalicylic_acid
Rv2681 2997953 c.1215C>G synonymous_variant 1.0 capreomycin
Rv3236c 3612721 c.395delT frameshift_variant 1.0 pyrazinamide Uncertain significance
lpqB 3623213 p.Trp566Cys missense_variant 1.0 bedaquiline
rifampicin
mtrB 3625250 p.Leu455Gln missense_variant 1.0 bedaquiline
rifampicin
mtrA 3627307 p.Ala15Ser missense_variant 1.0 bedaquiline
rifampicin
alr 3840445 p.Leu326Met missense_variant 1.0 cycloserine
alr 3841156 p.Leu89Val missense_variant 1.0 cycloserine
rpoA 3877966 p.Thr181Asn missense_variant 1.0 rifampicin
panD 4044216 c.65_66insT frameshift_variant 1.0 pyrazinamide Uncertain significance
glpK 4138295 p.Trp487Cys missense_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embB 4247289 p.Ala259Gly missense_variant 1.0 ethambutol
embB 4249154 p.Gly881Arg missense_variant 1.0 ethambutol
ubiA 4270024 c.-191T>G upstream_gene_variant 1.0 ethambutol