TB-Profiler result

Run: SRR19415697
Summary

Run ID: SRR19415697

Sample name:

Date: 2024-10-03T16:23:52.070385

Number of reads: 2112885

Percentage reads mapped: 99.62

Median coverage: 102.0

Strain: lineage1;lineage2.2.1;lineage3.1.1;lineage4.2.2.2

Spoligotype:

Drug-resistance: Other

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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 0.1
lineage3 East-African-Indian RD750 0.34
lineage2 East-Asian RD105 0.45
lineage3.1.1 East-African-Indian RD750 0.32
lineage4.2 Euro-American None 0.09
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.38
lineage2.2 East-Asian (Beijing) RD105;RD207 0.41
lineage4 Euro-American None 0.14
lineage1 Indo-Oceanic RD239 0.06
lineage4.2.2.2 Euro-American (Ural) None 0.08
lineage3.1 East-African-Indian RD750 0.38
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin gid c.351delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
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
gid 4407851 c.351delG frameshift_variant 0.19 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 8688 p.Ala463Ser missense_variant 0.12 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 13460 c.99T>C synonymous_variant 0.15 isoniazid Not assoc w R
Rv0010c 13605 c.-47G>T upstream_gene_variant 0.43 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.92 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.47 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.5 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.74 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.57 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.27 rifampicin Not assoc w R
rpoB 761489 c.1683G>A synonymous_variant 0.14 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 0.91 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 0.91 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.61 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.41 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.14 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.9 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 0.53 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 0.4 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
bacA 2062922 p.Ile603Val missense_variant 0.1 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 0.15 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.14 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.82 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.89 pyrazinamide Not assoc w R
PPE35 2168971 p.Ile548Val missense_variant 0.12 pyrazinamide Uncertain significance
PPE35 2170461 p.Gly51Glu missense_variant 0.44 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 0.18 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.3 pyrazinamide
eis 2714526 c.805_806delAC frameshift_variant 0.41 kanamycin Uncertain significance
amikacin Uncertain significance
ahpC 2726051 c.-142G>A upstream_gene_variant 0.14 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.31 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.3 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
Rv2681 2997599 c.861A>G synonymous_variant 0.14 capreomycin
Rv2752c 3065711 p.Gly161Ser missense_variant 0.51 levofloxacin Uncertain significance
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.98 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.1 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.51 pyrazinamide Not assoc w R - Interim
lpqB 3625039 c.-129C>G upstream_gene_variant 0.43 rifampicin
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 0.95 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626290 c.324C>G synonymous_variant 0.42 rifampicin
bedaquiline
mtrB 3626562 p.Pro18Ser missense_variant 0.48 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.13 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.27 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.24 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 4240172 p.Val104Met missense_variant 0.13 ethambutol Not assoc w R
embC 4241562 p.Arg567His missense_variant 0.23 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.35 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 0.35 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.12 ethambutol Not assoc w R
aftB 4267300 p.Pro513Ser missense_variant 0.12 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.5 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.15 ethambutol Not assoc w R
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 4338603 c.-82C>T upstream_gene_variant 0.12 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
whiB6 4338846 c.-325T>G upstream_gene_variant 0.17 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.8 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.31 streptomycin Not assoc w R