TB-Profiler result

Run: SRR1181252
Summary

Run ID: SRR1181252

Sample name:

Date: 2024-03-26T16:46:49.535698

Number of reads: 2879915

Percentage reads mapped: 99.12

Median coverage: 39.0

Strain: lineage2.2.1;lineage4.1.2;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 0.6
lineage4.1 Euro-American None 0.15
lineage4.1.2 Euro-American None 0.15
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.63
lineage2.2 East-Asian (Beijing) RD105;RD207 0.6
lineage4 Euro-American None 0.37
lineage4.8 Euro-American (mainly T) RD219 0.18
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 371 p.Pro124Leu missense_variant 0.23 isoniazid Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.82 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.78 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491556 c.774G>A synonymous_variant 0.52 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.59 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.47 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.69 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.54 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.59 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.62 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 0.76 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.81 clofazimine Not assoc w R
bedaquiline Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.64 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.16 capreomycin Not assoc w R
linezolid Not assoc w R
inhA 1674210 c.9A>C synonymous_variant 0.54 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.68 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.83 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 0.61 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.61 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
folC 2747022 p.Val193Ile missense_variant 0.22 para-aminosalicylic_acid
Rv2752c 3064519 c.1672delG frameshift_variant 0.54 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.7 cycloserine
Rv3083 3448894 p.Tyr131Asp missense_variant 0.31 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.72 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.84 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.62 bedaquiline Uncertain significance
rifampicin 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 0.73 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.65 ethambutol Not assoc w R
whiB6 4338286 p.Val79Ala missense_variant 0.79 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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 0.78 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.64 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.43 streptomycin Not assoc w R