TB-Profiler result

Run: SRR25827563
Summary

Run ID: SRR25827563

Sample name:

Date: 2024-10-05T10:47:12.731069

Number of reads: 8074936

Percentage reads mapped: 99.08

Median coverage: 274.0

Strain: lineage2.2.1.1;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 0.21
lineage2 East-Asian RD105 0.74
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.75
lineage2.2 East-Asian (Beijing) RD105;RD207 0.74
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.17
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.Ile317Val Uncertain significance Mutation from literature
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.Leu27Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 0.48 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.82 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.5 streptomycin Assoc w R
katG 2155163 p.Ile317Val missense_variant 0.13 isoniazid Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289162 p.Leu27Pro missense_variant 0.28 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.41 ethambutol Assoc w R
embB 4249518 p.His1002Arg missense_variant 0.14 ethambutol Uncertain significance Mutation from literature
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
dnaA 1332 c.1332A>C synonymous_variant 0.19 isoniazid Not assoc w R - Interim
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 13444 c.115T>C synonymous_variant 0.22 isoniazid Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.96 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.35 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.62 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 0.82 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.22 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.2 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.95 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 0.97 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.33 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.76 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 0.96 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 0.72 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 0.93 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471871 n.26C>T non_coding_transcript_exon_variant 0.17 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473609 n.-49G>C upstream_gene_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1673406 c.-796C>G upstream_gene_variant 0.2 isoniazid Uncertain significance
ethionamide Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.74 pyrazinamide Not assoc w R - Interim
tsnR 1854070 c.466_484delACCGGTAGCATCTTCGCGA frameshift_variant 0.18 linezolid Uncertain significance
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 0.98 isoniazid Not assoc w R
PPE35 2167802 c.2810delG frameshift_variant 0.15 pyrazinamide Uncertain significance
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
pncA 2289047 c.195C>T synonymous_variant 0.22 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.24 pyrazinamide
kasA 2518980 p.Arg289Thr missense_variant 0.15 isoniazid
eis 2714846 p.Val163Ile missense_variant 0.2 kanamycin Not assoc w R
amikacin Not assoc w R
folC 2747504 p.His32Arg missense_variant 0.2 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.26 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3569220 c.-541C>T upstream_gene_variant 0.19 kanamycin
amikacin
streptomycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.73 pyrazinamide Not assoc w R - Interim
lpqB 3623509 p.Val468Ile missense_variant 0.16 rifampicin Uncertain significance
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625228 c.1386G>A synonymous_variant 0.22 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.76 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640879 c.337C>T synonymous_variant 0.18 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpoA 3877960 p.Val183Gly missense_variant 0.14 rifampicin Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.25 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.21 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 4242056 p.Pro732Ala missense_variant 0.17 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.21 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 0.72 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.21 ethambutol
embB 4248115 c.1602C>T synonymous_variant 0.15 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.76 ethambutol Not assoc w R
ethA 4326474 p.Pro334Ala missense_variant 0.16 ethionamide Uncertain significance
ethA 4326676 p.Ser266Arg missense_variant 0.18 ethionamide Uncertain significance
ethA 4326735 p.Ala247Pro missense_variant 0.2 ethionamide Uncertain significance
whiB6 4338233 p.Ser97Pro missense_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338293 p.Ala77Ser missense_variant 0.2 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 0.95 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.77 streptomycin Not assoc w R