TB-Profiler result

Run: SRR25827356
Summary

Run ID: SRR25827356

Sample name:

Date: 2024-10-03T23:14:24.353197

Number of reads: 33416558

Percentage reads mapped: 97.25

Median coverage: 953.5

Strain: lineage2.2.1.1;lineage2.2.1.2;lineage3

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
lineage3 East-African-Indian RD750 0.28
lineage2 East-Asian RD105 0.71
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.7
lineage2.2 East-Asian (Beijing) RD105;RD207 0.7
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.21
lineage2.2.1.2 East-Asian (Beijing) RD105;RD207;RD181;RD142 0.28
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.His1002Arg Uncertain significance Mutation from literature
pyrazinamide pncA p.Thr76Pro Assoc w R
p.His57Tyr Assoc w R
p.Asp12Glu Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Ala504Thr Uncertain significance Mutation from literature
p.Val670Phe Uncertain significance Mutation from literature
ofloxacin
levofloxacin gyrB p.Ala504Thr Uncertain significance Mutation from literature
p.Val670Phe Uncertain significance Mutation from literature
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
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
gyrB 6749 p.Ala504Thr missense_variant 0.32 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
gyrB 7247 p.Val670Phe missense_variant 0.26 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.51 streptomycin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.2 streptomycin 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 2289016 p.Thr76Pro missense_variant 0.29 pyrazinamide Assoc w R
pncA 2289073 p.His57Tyr missense_variant 0.19 pyrazinamide Assoc w R
pncA 2289206 p.Asp12Glu missense_variant 0.29 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.35 ethambutol Assoc w R
embB 4249518 p.His1002Arg missense_variant 0.29 ethambutol Uncertain significance Mutation from literature
ethA 4326321 c.1152dupT frameshift_variant 0.28 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 7581 p.Asp94Ser missense_variant 0.28 levofloxacin
moxifloxacin
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 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.6 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 576508 c.1161C>A synonymous_variant 0.27 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.73 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657022 p.Glu150Val missense_variant 0.22 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.99 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.71 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.28 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.28 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764363 p.Gly332Ser missense_variant 0.31 rifampicin Uncertain significance
rpoC 766466 p.Glu1033Lys missense_variant 0.3 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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.63 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 778913 c.-433G>A upstream_gene_variant 0.22 bedaquiline
clofazimine
mmpS5 779615 c.-710C>G upstream_gene_variant 0.7 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253177 p.Thr453Met missense_variant 0.27 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
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 0.67 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 0.7 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 0.28 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
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 0.28 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.29 pyrazinamide
eis 2714846 p.Val163Ile missense_variant 0.21 kanamycin Not assoc w R
amikacin Not assoc w R
ahpC 2726105 c.-88G>A upstream_gene_variant 0.29 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.32 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
Rv2477c 2784442 c.-400G>A upstream_gene_variant 0.22 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2752c 3064843 p.Asp450Gly missense_variant 0.28 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
thyX 3067948 c.-3G>T upstream_gene_variant 0.26 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.7 pyrazinamide Not assoc w R - Interim
lpqB 3623174 c.1737G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
bedaquiline 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 0.71 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3841473 c.-53G>A upstream_gene_variant 0.29 cycloserine
rpoA 3877687 p.Glu274Gly missense_variant 0.3 rifampicin Uncertain significance
rpoA 3878618 c.-111A>C upstream_gene_variant 0.19 rifampicin
clpC1 4040249 p.Glu152Asp missense_variant 0.13 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.24 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.27 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 4242039 p.Ala726Gly missense_variant 0.29 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.25 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243190 c.-43G>C upstream_gene_variant 0.31 ethambutol Uncertain significance
embA 4243216 c.-17G>A upstream_gene_variant 0.2 ethambutol Uncertain significance
embA 4243460 c.228C>T synonymous_variant 0.69 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.22 ethambutol
embB 4247039 p.Phe176Val missense_variant 0.17 ethambutol
embB 4248115 c.1602C>T synonymous_variant 0.22 ethambutol Not assoc w R
aftB 4267492 p.Ala449Thr missense_variant 0.25 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.68 ethambutol Not assoc w R
ethA 4326929 p.Gly182Asp missense_variant 0.28 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 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.7 streptomycin Not assoc w R
gid 4407967 p.Leu79Trp missense_variant 0.29 streptomycin Uncertain significance