TB-Profiler result

Run: SRR25827547
Summary

Run ID: SRR25827547

Sample name:

Date: 2024-10-04T18:38:36.627828

Number of reads: 17413514

Percentage reads mapped: 99.21

Median coverage: 461.0

Strain: lineage2.2.1;lineage3.1.2

Spoligotype:

Drug-resistance: XDR-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 0.39
lineage3.1.2 East-African-Indian RD750 0.35
lineage2 East-Asian RD105 0.61
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.63
lineage2.2 East-Asian (Beijing) RD105;RD207 0.62
lineage3.1 East-African-Indian RD750 0.37
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
p.Ile480Val Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
embB p.Met306Val Assoc w R
pyrazinamide pncA p.Ile5Ser Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.His70Arg Uncertain significance Mutation from literature
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.His70Arg Uncertain significance Mutation from literature
p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin eis c.-14C>T Assoc w R - Interim Can only confer resistance if genetically linked to a functional Eis
capreomycin tlyA c.590_591delTG Assoc w R
kanamycin eis c.-14C>T Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine
ethionamide ethA c.80_81delGCinsA Assoc w R
clofazimine mmpR5 c.136delT Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid thyA p.Thr22Ala Mutation from literature
delamanid
bedaquiline mmpR5 c.136delT Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
linezolid rrl n.2270G>T Assoc w R - Interim
n.2814G>T Assoc w R - Interim
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 7510 p.His70Arg missense_variant 0.61 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
gyrA 7570 p.Ala90Val missense_variant 0.6 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)
rpoB 761155 p.Ser450Leu missense_variant 0.69 rifampicin Assoc w R
rpoB 761244 p.Ile480Val missense_variant 0.64 rifampicin Uncertain significance Mutation from literature
mmpR5 779124 c.136delT frameshift_variant 0.62 bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
rpsL 781687 p.Lys43Arg missense_variant 0.59 streptomycin Assoc w R
rrl 1475927 n.2270G>T non_coding_transcript_exon_variant 0.59 linezolid Assoc w R - Interim
rrl 1476471 n.2814G>T non_coding_transcript_exon_variant 0.59 linezolid Assoc w R - Interim
tlyA 1918527 c.590_591delTG frameshift_variant 0.61 capreomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.62 isoniazid Assoc w R High-level resistance
pncA 2289228 p.Ile5Ser missense_variant 0.6 pyrazinamide Assoc w R
eis 2715346 c.-14C>T upstream_gene_variant 0.58 amikacin Assoc w R - Interim Can only confer resistance if genetically linked to a functional Eis
kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
thyA 3074408 p.Thr22Ala missense_variant 0.55 para-aminosalicylic_acid Mutation from literature
embA 4243217 c.-16C>T upstream_gene_variant 0.59 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.65 ethambutol Assoc w R
ethA 4327393 c.80_81delGCinsA frameshift_variant&stop_gained 0.54 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 491290 p.Val170Met missense_variant 0.62 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.67 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.63 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.99 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.58 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.35 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.38 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.62 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.62 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 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 0.56 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473543 n.-115C>T upstream_gene_variant 0.41 capreomycin
linezolid
rpsA 1834177 c.636A>C synonymous_variant 0.61 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
katG 2156482 c.-371G>A upstream_gene_variant 0.35 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.4 pyrazinamide Not assoc w R
PPE35 2170214 c.399C>A synonymous_variant 0.36 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.37 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.39 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.38 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.39 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
thyX 3067949 c.-4C>T upstream_gene_variant 0.62 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449861 c.1360dupC frameshift_variant 0.61 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.65 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 0.59 rifampicin Not assoc w R
bedaquiline Uncertain significance
panD 4044340 c.-59G>T upstream_gene_variant 0.37 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.38 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.38 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.6 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.34 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 0.6 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.21 ethambutol
embB 4247033 p.Ser174Arg missense_variant 0.14 ethambutol
embB 4247039 p.Phe176Val missense_variant 0.19 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.64 ethambutol Not assoc w R
whiB6 4338238 p.Leu95Arg missense_variant 0.6 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 1.0 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.66 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.63 streptomycin Not assoc w R