TB-Profiler result

Run: SRR25827650
Summary

Run ID: SRR25827650

Sample name:

Date: 2024-05-20T10:04:04.495486

Number of reads: 3834030

Percentage reads mapped: 99.19

Median coverage: 123.0

Strain: lineage2.2.1;lineage3;lineage4.1.2;lineage4.2.2;lineage4.9

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
lineage4.2.2 Euro-American (Ural) None 0.07
lineage3 East-African-Indian RD750 0.34
lineage2 East-Asian RD105 0.35
lineage4.1.2 Euro-American None 0.09
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.31
lineage2.2 East-Asian (Beijing) RD105;RD207 0.37
lineage4 Euro-American None 0.3
lineage4.9 Euro-American (H37Rv-like) None 0.09
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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Gly132Ala 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.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Gly 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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 7570 p.Ala90Val missense_variant 0.18 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 7582 p.Asp94Gly missense_variant 0.43 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.57 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.35 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.42 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.27 isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R Alias fabG1_c.-15C>T
katG 2155168 p.Ser315Thr missense_variant 0.56 isoniazid Assoc w R High-level resistance
pncA 2288847 p.Gly132Ala missense_variant 0.14 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.27 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.19 ethambutol 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 0.88 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.9 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.93 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.21 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.71 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.33 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.37 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.69 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.34 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.37 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.41 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.7 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.14 rifampicin Uncertain significance
rpoC 764840 p.Ile491Val missense_variant 0.15 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 0.93 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.78 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.31 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.4 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 0.92 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.14 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.77 isoniazid Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
levofloxacin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.29 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 0.97 kanamycin
amikacin
streptomycin
capreomycin
rpsA 1834177 c.636A>C synonymous_variant 0.36 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.92 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.92 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.77 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.75 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.94 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 0.4 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.33 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.31 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.38 kanamycin Not assoc w R
moxifloxacin Not assoc w R
amikacin Not assoc w R
rifampicin Not assoc w R
streptomycin Not assoc w R - Interim
ethambutol Not assoc w R
levofloxacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.91 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.42 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.94 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626224 c.390G>A synonymous_variant 0.2 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.37 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3841473 c.-53G>A upstream_gene_variant 0.33 cycloserine
panD 4044872 c.-591C>T upstream_gene_variant 0.36 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.37 isoniazid Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
streptomycin Not assoc w R - Interim
ethambutol Not assoc w R
levofloxacin Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.25 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.31 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.93 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.37 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.33 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 0.92 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.94 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.81 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.2 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.39 streptomycin Not assoc w R