TB-Profiler result

Run: SRR25827363
Summary

Run ID: SRR25827363

Sample name:

Date: 2024-03-25T20:10:52.621072

Number of reads: 23241326

Percentage reads mapped: 88.37

Median coverage: 145.0

Strain: lineage2.2.1;lineage3

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 0.71
lineage2 East-Asian RD105 0.29
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.33
lineage2.2 East-Asian (Beijing) RD105;RD207 0.3
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 p.Gly132Ala Assoc w R
p.Leu27Pro Assoc w R
p.Asp12Glu Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
gid c.351delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide ethA c.1152dupT Assoc w R
c.87delC 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
rpoB 761155 p.Ser450Leu missense_variant 0.86 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.14 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.43 kanamycin Assoc w R
capreomycin Assoc w R
amikacin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288847 p.Gly132Ala missense_variant 0.18 pyrazinamide Assoc w R
pncA 2289162 p.Leu27Pro missense_variant 0.15 pyrazinamide Assoc w R
pncA 2289206 p.Asp12Glu missense_variant 0.36 pyrazinamide Assoc w R
ethA 4326321 c.1152dupT frameshift_variant 0.39 ethionamide Assoc w R
ethA 4327386 c.87delC frameshift_variant 0.24 ethionamide Assoc w R
gid 4407851 c.351delG frameshift_variant 0.2 streptomycin 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 7581 p.Asp94Cys missense_variant 0.22 levofloxacin
moxifloxacin
gyrA 7585 p.Ser95Thr missense_variant 0.99 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 491290 p.Val170Met missense_variant 0.17 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.34 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.35 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.66 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.61 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 766466 p.Glu1033Lys missense_variant 0.42 rifampicin Uncertain significance
rpoC 766488 p.Pro1040Arg missense_variant 0.19 rifampicin Uncertain significance
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 1.0 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 0.29 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253177 p.Thr453Met missense_variant 0.37 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1253566 c.969A>G synonymous_variant 0.25 moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 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 0.3 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1416814 c.534G>A synonymous_variant 0.24 ethambutol Not assoc w R
embR 1417190 p.Asp53Gly missense_variant 0.31 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473368 n.1523G>A non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.34 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 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2222700 c.465C>T synonymous_variant 0.46 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
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 0.72 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.69 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.68 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.71 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568857 c.-178C>T upstream_gene_variant 0.26 streptomycin Uncertain significance
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
whiB7 3569220 c.-541C>T upstream_gene_variant 0.17 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.29 pyrazinamide Not assoc w R - Interim
lpqB 3623174 c.1737G>C synonymous_variant 0.46 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.94 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.28 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841473 c.-53G>A upstream_gene_variant 0.37 cycloserine
panD 4044023 c.259C>T synonymous_variant 0.17 pyrazinamide Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.73 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.78 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
glpK 4139633 c.123C>A synonymous_variant 0.18 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
embC 4242075 p.Arg738Gln missense_variant 0.73 ethambutol 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 0.28 ethambutol Not assoc w R
embB 4247429 c.916_918delATGinsGA frameshift_variant&missense_variant 0.17 ethambutol
aftB 4267492 p.Ala449Thr missense_variant 0.4 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.4 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.15 ethionamide Uncertain significance
ethA 4326762 p.Val238Ile missense_variant 0.17 ethionamide 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 0.99 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.21 streptomycin Not assoc w R
gid 4407967 p.Leu79Trp missense_variant 0.55 streptomycin Uncertain significance