TB-Profiler result

Run: SRR7516439
Summary

Run ID: SRR7516439

Sample name:

Date: 2024-04-15T17:52:11.429142

Number of reads: 2438232

Percentage reads mapped: 99.55

Median coverage: 69.0

Strain: lineage2.2.1;lineage4.2.1.1

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 0.8
lineage4.2 Euro-American None 0.17
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.8
lineage2.2 East-Asian (Beijing) RD105;RD207 0.79
lineage4 Euro-American None 0.19
lineage4.2.1.1 Euro-American (TUR) None 0.18
lineage4.2.1 Euro-American (TUR) None 0.19
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu430Pro Assoc w R
p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Ser347Ile Uncertain significance Mutation from literature
p.Gln497Arg Assoc w R
pyrazinamide pncA c.-11A>G Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-37G>T Assoc w R
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA c.380dupG 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 7570 p.Ala90Val missense_variant 0.87 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rpoB 761095 p.Leu430Pro missense_variant 0.78 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.16 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.64 streptomycin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.86 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.77 isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R Alias fabG1_c.-15C>T
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289252 c.-11A>G upstream_gene_variant 0.27 pyrazinamide Assoc w R
eis 2715369 c.-37G>T upstream_gene_variant 0.76 kanamycin Assoc w R
embB 4247553 p.Ser347Ile missense_variant 0.81 ethambutol Uncertain significance Mutation from literature
embB 4248003 p.Gln497Arg missense_variant 0.36 ethambutol Assoc w R
ethA 4327093 c.380dupG frameshift_variant 0.89 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 1.0 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 491742 c.960T>C synonymous_variant 0.82 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.79 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.8 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.85 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.87 ethionamide Uncertain significance
rpoB 760315 p.Val170Ala missense_variant 0.78 rifampicin Uncertain significance
rpoB 760728 p.Tyr308Asp missense_variant 0.61 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.75 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.84 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 0.84 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.69 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 777451 p.Val344Leu missense_variant 0.28 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.77 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.12 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.73 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.85 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.87 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.79 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 0.16 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.82 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.78 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
ald 3086742 c.-78A>C upstream_gene_variant 0.24 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.77 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.99 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.79 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 0.86 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.76 ethambutol Not assoc w R
whiB6 4338563 c.-42G>T upstream_gene_variant 0.76 capreomycin Not assoc w R
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 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.83 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.84 streptomycin Not assoc w R
gid 4408213 c.-11C>T upstream_gene_variant 0.26 streptomycin Uncertain significance