TB-Profiler result

Run: SRR25827428
Summary

Run ID: SRR25827428

Sample name:

Date: 2024-04-15T13:23:08.962542

Number of reads: 6526424

Percentage reads mapped: 99.15

Median coverage: 199.0

Strain: lineage2.2.1;lineage3;lineage4

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.72
lineage2 East-Asian RD105 0.21
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.2
lineage2.2 East-Asian (Beijing) RD105;RD207 0.2
lineage4 Euro-American None 0.07
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
rpoC p.Leu527Val Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg 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
rpoB 761155 p.Ser450Leu missense_variant 0.34 rifampicin Assoc w R
rpoC 764948 p.Leu527Val missense_variant 0.14 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.28 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.41 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 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
gyrA 9629 c.2328C>T synonymous_variant 0.6 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
fgd1 491290 p.Val170Met missense_variant 0.16 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.93 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.28 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.21 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.95 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.2 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.67 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.74 rifampicin Not assoc w R
rpoB 762441 c.2635C>T synonymous_variant 0.69 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.93 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.99 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.92 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.21 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.19 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.98 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.23 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 0.29 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
katG 2154724 p.Arg463Leu missense_variant 0.95 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.93 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
pncA 2289047 c.195C>T synonymous_variant 0.74 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.74 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.67 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.72 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
ribD 2986827 c.-12G>A upstream_gene_variant 0.16 para-aminosalicylic_acid
Rv2752c 3066143 p.Arg17Trp missense_variant 0.58 ethambutol Uncertain significance
moxifloxacin
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.15 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 0.17 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878544 c.-37C>G upstream_gene_variant 0.71 rifampicin
panD 4044872 c.-591C>T upstream_gene_variant 0.67 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.69 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.14 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.65 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.99 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.21 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.2 ethambutol
embB 4247429 c.916_918delATGinsGA frameshift_variant&missense_variant 0.14 ethambutol
embB 4248216 p.Arg568Pro missense_variant 0.59 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.24 ethambutol Not assoc w R
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 0.94 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.17 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.23 streptomycin Not assoc w R