TB-Profiler result

Run: SRR14782170
Summary

Run ID: SRR14782170

Sample name:

Date: 2024-10-04T23:34:27.242963

Number of reads: 3877218

Percentage reads mapped: 99.6

Median coverage: 119.0

Strain: lineage2.2.1;lineage4.8

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.12
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.14
lineage2.2 East-Asian (Beijing) RD105;RD207 0.12
lineage4 Euro-American None 0.88
lineage4.8 Euro-American (mainly T) RD219 0.88
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
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
katG 2155168 p.Ser315Thr missense_variant 0.13 isoniazid Assoc w R High-level resistance
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 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.15 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.11 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.1 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.1 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 776182 p.Asp767Asn missense_variant 0.17 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.11 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 0.14 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 0.19 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.9 capreomycin Not assoc w R
linezolid Not assoc w R
inhA 1673249 c.-953C>A upstream_gene_variant 0.9 isoniazid
ethionamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
tlyA 1918346 p.Ala136Val missense_variant 0.85 capreomycin
katG 2154724 p.Arg463Leu missense_variant 0.12 isoniazid Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.91 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 0.87 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.11 cycloserine
lpqB 3624235 p.Gly226Arg missense_variant 0.9 rifampicin
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 0.11 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.14 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3642321 p.Val263Ile missense_variant 0.9 pretomanid
delamanid
clofazimine
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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R