TB-Profiler result

Run: SRR25827306
Summary

Run ID: SRR25827306

Sample name:

Date: 2024-04-15T23:22:53.729589

Number of reads: 7391170

Percentage reads mapped: 98.86

Median coverage: 249.0

Strain: lineage2.2.1;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 0.33
lineage2 East-Asian RD105 0.65
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.63
lineage2.2 East-Asian (Beijing) RD105;RD207 0.64
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
pyrazinamide pncA p.Thr177Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
gid c.102delG 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.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Ala Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid thyX c.-16C>T Mutation from literature
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 0.35 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.Asp94Ala missense_variant 0.5 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.68 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.63 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.74 isoniazid Assoc w R High-level resistance
pncA 2288713 p.Thr177Pro missense_variant 0.36 pyrazinamide Assoc w R
thyX 3067961 c.-16C>T upstream_gene_variant 0.44 para-aminosalicylic_acid Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.6 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 0.32 streptomycin 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
Rv0010c 13630 c.-72G>A upstream_gene_variant 0.23 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.98 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.63 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620553 c.663T>C synonymous_variant 0.23 capreomycin Not assoc w R
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.65 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.97 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.7 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.25 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.3 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.96 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.25 rifampicin Uncertain significance
rpoC 764840 p.Ile491Val missense_variant 0.34 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.96 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.62 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.61 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.95 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.66 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.6 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 0.96 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.99 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 0.33 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.35 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.26 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.38 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2477c 2784204 c.-162A>C upstream_gene_variant 0.3 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2784389 c.-347T>C upstream_gene_variant 0.33 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.69 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.69 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640211 c.-332T>G upstream_gene_variant 0.21 clofazimine
pretomanid
delamanid
fbiB 3642627 p.Arg365Gly missense_variant 0.36 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
alr 3841473 c.-53G>A upstream_gene_variant 0.33 cycloserine
clpC1 4039180 p.Arg509Gly missense_variant 0.3 pyrazinamide Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.29 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.27 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240861 c.999G>A synonymous_variant 0.23 ethambutol Not assoc w R - Interim
embC 4241022 p.Ala387Val missense_variant 0.34 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.31 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 0.71 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.19 ethambutol
embB 4248554 p.Gly681Ser missense_variant 0.3 ethambutol
embB 4249757 p.Thr1082Ala missense_variant 0.29 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.69 ethambutol Not assoc w R
ubiA 4269296 p.Met180Val missense_variant 0.34 ethambutol Uncertain significance
whiB6 4338365 p.Cys53Gly missense_variant 0.38 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.96 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.32 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.63 streptomycin Not assoc w R