TB-Profiler result

Run: SRR29539513
Summary

Run ID: SRR29539513

Sample name:

Date: 2025-02-11T19:42:28.670875

Number of reads: 3193736

Percentage reads mapped: 99.68

Median coverage: 99.0

Strain: lineage2.2.1;lineage4.8

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.21
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.19
lineage2.2 East-Asian (Beijing) RD105;RD207 0.19
lineage4 Euro-American None 0.79
lineage4.8 Euro-American (mainly T) RD219 0.8
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide pncA c.524delT Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Asn Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Asn Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA p.Gln347* Assoc w R
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
gyrA 7581 p.Asp94Asn missense_variant 0.17 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.21 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.17 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.2 isoniazid Assoc w R High-level resistance
pncA 2288717 c.524delT frameshift_variant 0.19 pyrazinamide Assoc w R
ethA 4326435 p.Gln347* stop_gained 0.16 ethionamide 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
gyrA 7585 p.Ser95Thr missense_variant 0.16 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.22 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.18 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.26 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.15 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin 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 0.19 ethionamide Uncertain significance
Rv0565c 657230 p.Ala81Thr missense_variant 0.18 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.17 rifampicin Not assoc w R
rpoC 764824 p.Asp485Glu missense_variant 0.16 rifampicin
rpoC 764825 p.Val486Leu missense_variant 0.17 rifampicin
rpoC 765369 p.Thr667Met missense_variant 0.73 rifampicin Uncertain significance
rpoC 767288 c.3919C>T synonymous_variant 0.79 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
mmpL5 776100 p.Thr794Ile missense_variant 0.19 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.25 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.17 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 0.21 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 0.16 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 0.75 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.19 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 0.19 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.22 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
ald 3086731 c.-89A>G upstream_gene_variant 0.23 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.19 cycloserine
ald 3087629 p.Asp270Glu missense_variant 0.18 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.25 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.2 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.23 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 0.21 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.12 ethambutol Not assoc w R
whiB6 4338371 p.Thr51Pro missense_variant 0.18 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338547 c.-27delG upstream_gene_variant 0.88 kanamycin
capreomycin
amikacin
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 0.14 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.19 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.19 streptomycin Not assoc w R