TB-Profiler result

Run: ERR176557
Summary

Run ID: ERR176557

Sample name:

Date: 2024-10-05T00:19:34.979036

Number of reads: 4844068

Percentage reads mapped: 88.54

Median coverage: 111.0

Strain: lineage4.3.4.1

Spoligotype:

Drug-resistance: Sensitive

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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 0.94
lineage4.3.4.1 Euro-American (LAM) RD174 0.87
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.95
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
Rv0010c 13483 p.Ala26Thr missense_variant 0.91 isoniazid Uncertain significance
nusG 734532 c.279A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
nusG 734559 c.306T>C synonymous_variant 0.12 rifampicin
rpoB 762143 c.2337T>C synonymous_variant 0.13 rifampicin
rpoB 762161 c.2355C>G synonymous_variant 0.12 rifampicin
rpoB 762185 c.2379G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764293 c.924G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764320 c.951C>T synonymous_variant 0.15 rifampicin
rpoC 764338 c.969G>A synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.94 rifampicin Not assoc w R
rpoC 765452 p.Ala695Ser missense_variant 0.12 rifampicin
rpoC 765734 c.2365T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.13 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.15 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
sigE 1364434 p.Arg8Trp missense_variant 0.84 pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1473899 n.242A>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
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
Rv1979c 2222854 p.Ile104Thr missense_variant 0.89 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2477c 2783254 c.789A>G synonymous_variant 0.13 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783263 c.780G>C synonymous_variant 0.13 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783275 c.768C>G synonymous_variant 0.12 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
thyA 3073868 p.Thr202Ala missense_variant 0.93 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.92 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.89 pyrazinamide Not assoc w R
clpC1 4039991 c.714G>A synonymous_variant 0.85 pyrazinamide Not assoc w R
embC 4241167 c.1305C>G synonymous_variant 0.12 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 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 4408156 p.Leu16Arg missense_variant 0.93 streptomycin Not assoc w R