TB-Profiler result

Run: SRR29096499
Summary

Run ID: SRR29096499

Sample name:

Date: 2025-02-11T18:20:15.542154

Number of reads: 3629838

Percentage reads mapped: 99.29

Median coverage: 122.0

Strain: lineage2.2.1;lineage4.2.2.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.25
lineage2 East-Asian RD105 0.77
lineage4.2 Euro-American None 0.24
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.77
lineage2.2 East-Asian (Beijing) RD105;RD207 0.78
lineage4 Euro-American None 0.22
lineage4.2.2.2 Euro-American (Ural) None 0.21
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 embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Thr160Ala Not assoc w R - Interim Mutation from literature
p.Thr100Ile Uncertain significance Mutation from literature
streptomycin rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA p.Gly43Cys Uncertain significance Mutation from literature
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
rpoB 761155 p.Ser450Leu missense_variant 0.77 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.78 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.8 isoniazid Assoc w R High-level resistance
pncA 2288764 p.Thr160Ala missense_variant 0.85 pyrazinamide Not assoc w R - Interim Mutation from literature
pncA 2288943 p.Thr100Ile missense_variant 0.8 pyrazinamide Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.76 ethambutol Assoc w R
ethA 4327347 p.Gly43Cys missense_variant 0.77 ethionamide Uncertain significance Mutation from literature
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 8688 p.Ala463Ser missense_variant 0.18 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
fgd1 491328 c.546C>G synonymous_variant 0.75 pretomanid
delamanid
clofazimine
fgd1 491330 p.Lys183Met missense_variant 0.76 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.8 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.75 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 576077 c.730C>T synonymous_variant 0.3 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.8 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.79 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.84 ethionamide Uncertain significance
Rv0565c 657425 p.Gly16Ser missense_variant 0.24 ethionamide Uncertain significance
rpoB 761489 c.1683G>A synonymous_variant 0.21 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.78 rifampicin Not assoc w R
rpoC 764822 p.Asp485Tyr missense_variant 0.73 rifampicin Uncertain significance
mmpL5 775592 c.2889G>A synonymous_variant 0.78 bedaquiline Not assoc w R - Interim
clofazimine 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 0.72 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.76 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.76 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.21 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.74 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 0.75 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.75 pyrazinamide Not assoc w R - Interim
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
bacA 2063685 c.1044G>A synonymous_variant 0.23 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.23 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.74 isoniazid Not assoc w R
katG 2156513 c.-402A>C upstream_gene_variant 0.28 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.8 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
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.18 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086742 c.-78A>C upstream_gene_variant 0.22 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449315 p.Trp271* stop_gained 0.79 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.8 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.74 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 0.71 ethambutol Not assoc w R
embB 4247717 p.Leu402Val missense_variant 0.8 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.8 ethambutol Not assoc w R
whiB6 4338365 p.Cys53Arg missense_variant 0.79 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 4407588 c.615A>G synonymous_variant 0.86 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.74 streptomycin Not assoc w R