TB-Profiler result

Run: SRR19415531
Summary

Run ID: SRR19415531

Sample name:

Date: 2024-04-15T22:38:23.814505

Number of reads: 1399106

Percentage reads mapped: 99.51

Median coverage: 67.0

Strain: lineage1.1.2;lineage2.2.1;lineage3.1.1;lineage4

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.18
lineage1.1.2 Indo-Oceanic RD239 0.56
lineage2 East-Asian RD105 0.13
lineage3.1.1 East-African-Indian RD750 0.15
lineage1.1 Indo-Oceanic RD239 0.59
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.1
lineage2.2 East-Asian (Beijing) RD105;RD207 0.16
lineage4 Euro-American None 0.11
lineage1 Indo-Oceanic RD239 0.63
lineage3.1 East-African-Indian RD750 0.12
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
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
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
gyrB 6112 p.Met291Ile missense_variant 0.56 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.51 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 8452 p.Ala384Val missense_variant 0.72 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.64 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 13298 p.Ile87Met missense_variant 0.49 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.45 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.88 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.26 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.61 ethionamide
nusG 734102 c.-152G>T upstream_gene_variant 0.51 rifampicin
nusG 734116 c.-138T>C upstream_gene_variant 0.43 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.15 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.88 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.66 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.66 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.56 rifampicin Not assoc w R
rpoC 767094 p.Ser1242Asn missense_variant 0.17 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 0.9 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.15 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 779331 c.-851C>T upstream_gene_variant 0.59 clofazimine
bedaquiline
mmpS5 779615 c.-710C>G upstream_gene_variant 0.18 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.58 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.92 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.65 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.48 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.62 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
fabG1 1673283 c.-157A>C upstream_gene_variant 0.69 ethionamide
isoniazid
tsnR 1853974 c.369C>T synonymous_variant 0.71 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.7 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917777 c.-163A>G upstream_gene_variant 0.57 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.61 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.93 isoniazid Not assoc w R
katG 2155557 c.555C>T synonymous_variant 0.59 isoniazid Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 0.83 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.51 pyrazinamide Uncertain significance
PPE35 2170461 p.Gly51Glu missense_variant 0.22 pyrazinamide Not assoc w R
Rv1979c 2221783 p.Ala461Glu missense_variant 0.67 clofazimine
bedaquiline Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.54 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
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 0.12 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.13 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.57 isoniazid
eis 2714526 c.805_806delAC frameshift_variant 0.2 amikacin Uncertain significance
kanamycin Uncertain significance
ahpC 2726051 c.-142G>A upstream_gene_variant 0.57 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.21 isoniazid Not assoc w R
ahpC 2726672 c.480G>A synonymous_variant 0.55 isoniazid Not assoc w R - Interim
Rv2477c 2782498 c.1545C>T synonymous_variant 0.24 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
Rv2681 2996912 c.174C>T synonymous_variant 0.52 capreomycin Not assoc w R
Rv2752c 3064532 p.Thr554Ala missense_variant 0.56 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.51 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv2752c 3064674 c.1518C>T synonymous_variant 0.55 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065711 p.Gly161Ser missense_variant 0.21 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.55 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.56 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3625039 c.-129C>G upstream_gene_variant 0.11 bedaquiline
rifampicin
mtrB 3625065 p.Met517Leu missense_variant 0.93 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.6 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.17 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.52 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.62 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.69 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.14 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 0.18 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.62 ethambutol Not assoc w R
embA 4245166 p.Pro645Gln missense_variant 0.52 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.56 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.5 ethambutol Not assoc w R
aftB 4267300 p.Pro513Ser missense_variant 0.13 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.11 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.68 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.66 ethambutol Not assoc w R
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 4338603 c.-82C>T upstream_gene_variant 0.51 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
whiB6 4338846 c.-325T>G upstream_gene_variant 0.13 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.91 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.74 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.16 streptomycin Not assoc w R