TB-Profiler result

Run: SRR25827530
Summary

Run ID: SRR25827530

Sample name:

Date: 2024-10-04T19:55:47.117596

Number of reads: 18676137

Percentage reads mapped: 99.14

Median coverage: 558.0

Strain: lineage2.2.1;lineage4

Spoligotype:

Drug-resistance: 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 0.93
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.93
lineage2.2 East-Asian (Beijing) RD105;RD207 0.92
lineage4 Euro-American None 0.06
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.Met306Val Assoc w R
p.Gly406Ser Assoc w R
p.Gln853Pro Uncertain significance Mutation from literature
pyrazinamide pncA p.Asp63Ala Assoc w R
c.-11A>G Assoc w R
streptomycin rpsL p.Lys43Arg 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)
p.Asp94Tyr Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Tyr Assoc w R
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.1047dupT Assoc w R
clofazimine
para-aminosalicylic_acid thyX c.-16C>T Mutation from literature
delamanid
bedaquiline
linezolid rplC p.Cys154Arg Assoc w R
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 0.46 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7581 p.Asp94Tyr missense_variant 0.4 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin Assoc w R
rplC 801268 p.Cys154Arg missense_variant 0.39 linezolid Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.29 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid Assoc w R High-level resistance
pncA 2289054 p.Asp63Ala missense_variant 0.37 pyrazinamide Assoc w R
pncA 2289252 c.-11A>G upstream_gene_variant 0.36 pyrazinamide Assoc w R
thyX 3067961 c.-16C>T upstream_gene_variant 0.36 para-aminosalicylic_acid Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.46 ethambutol Assoc w R
embB 4247729 p.Gly406Ser missense_variant 0.39 ethambutol Assoc w R
embB 4249071 p.Gln853Pro missense_variant 0.41 ethambutol Uncertain significance Mutation from literature
ethA 4326426 c.1047dupT frameshift_variant 0.38 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 7283 c.-19G>T upstream_gene_variant 0.43 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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
Rv0010c 13641 c.-83A>G upstream_gene_variant 0.31 isoniazid Uncertain significance
fgd1 491290 p.Val170Met missense_variant 0.48 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.95 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.93 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.93 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.95 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.92 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.96 rifampicin Not assoc w R
rpoC 764666 p.Gly433Ser missense_variant 0.8 rifampicin Uncertain significance
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 0.94 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.92 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.93 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253930 p.Phe202Tyr missense_variant 0.4 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.94 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 0.94 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 0.91 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.99 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 0.94 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
pepQ 2860365 c.54G>T synonymous_variant 0.41 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
Rv2752c 3066004 p.Asp63Ala missense_variant 0.34 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
thyA 3074069 p.Val135Phe missense_variant 0.33 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568425 c.255T>G synonymous_variant 0.19 kanamycin
amikacin
streptomycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.94 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 0.92 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4241022 p.Ala387Val missense_variant 0.5 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243217 c.-16C>A upstream_gene_variant 0.37 ethambutol Uncertain significance
embA 4243460 c.228C>T synonymous_variant 0.91 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.18 ethambutol
embB 4249757 p.Thr1082Ala missense_variant 0.47 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.93 ethambutol Not assoc w R
ubiA 4269311 p.Trp175Gly missense_variant 0.39 ethambutol Uncertain significance
ethA 4326900 p.Pro192Thr missense_variant 0.43 ethionamide 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 0.93 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.46 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.93 streptomycin Not assoc w R