TB-Profiler result

Run: SRR23862086
Summary

Run ID: SRR23862086

Sample name:

Date: 2024-10-04T06:15:09.330809

Number of reads: 4427156

Percentage reads mapped: 99.69

Median coverage: 127.0

Strain: lineage2.2.1;lineage4.8

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.16
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.15
lineage2.2 East-Asian (Beijing) RD105;RD207 0.15
lineage4 Euro-American None 0.84
lineage4.8 Euro-American (mainly T) RD219 0.86
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 gid c.102delG Assoc w R
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
gid 4408100 c.102delG frameshift_variant 0.9 streptomycin 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
fgd1 491742 c.960T>C synonymous_variant 0.14 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.11 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.13 ethionamide Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.12 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.13 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 0.12 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.14 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.14 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 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.75 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.11 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 0.14 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.13 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.93 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.84 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.18 cycloserine
Rv3083 3448322 c.-182G>A upstream_gene_variant 0.88 ethionamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.18 pyrazinamide Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.12 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.15 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.12 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
gid 4407927 p.Glu92Asp missense_variant 0.15 streptomycin Not assoc w R