TB-Profiler result

Run: SRR19428598
Summary

Run ID: SRR19428598

Sample name:

Date: 2024-10-03T16:23:54.209426

Number of reads: 2057301

Percentage reads mapped: 99.45

Median coverage: 103.0

Strain: lineage1.1.2;lineage2.2.1;lineage3.1.1;lineage4.6.1

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 0.44
lineage1.1.2 Indo-Oceanic RD239 0.23
lineage4.6 Euro-American None 0.08
lineage2 East-Asian RD105 0.06
lineage3.1.1 East-African-Indian RD750 0.36
lineage1.1 Indo-Oceanic RD239 0.27
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.09
lineage2.2 East-Asian (Beijing) RD105;RD207 0.13
lineage4 Euro-American None 0.2
lineage1 Indo-Oceanic RD239 0.26
lineage4.6.1 Euro-American (Uganda) RD724 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
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 0.38 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.4 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 0.35 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.27 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 0.36 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.42 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.81 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575080 c.-268A>G upstream_gene_variant 0.13 isoniazid Uncertain significance
ethionamide Uncertain significance
ccsA 620625 p.Ile245Met missense_variant 0.12 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.45 ethionamide Not assoc w R - Interim
Rv0565c 657425 p.Gly16Ser missense_variant 0.11 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.29 ethionamide
hadA 732154 c.225G>C synonymous_variant 0.21 isoniazid Not assoc w R - Interim
nusG 734116 c.-138T>C upstream_gene_variant 0.26 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.29 rifampicin Not assoc w R
rpoB 760948 p.Asn381Ser missense_variant 0.1 rifampicin
rpoB 761489 c.1683G>A synonymous_variant 0.12 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.38 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.93 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.27 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.27 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.23 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 0.73 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.13 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
rplC 800250 c.-559C>G upstream_gene_variant 0.12 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.3 linezolid Not assoc w R
Rv1129c 1254253 c.282C>T synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.75 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254732 c.-198C>T upstream_gene_variant 0.17 levofloxacin
moxifloxacin
isoniazid
rifampicin
fbiC 1303646 p.Ala239Glu missense_variant 0.2 pretomanid
delamanid
clofazimine
Rv1258c 1406760 c.580_581insC frameshift_variant 0.12 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.25 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.34 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.29 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.2 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.17 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 0.16 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.16 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.75 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.86 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.31 pyrazinamide Uncertain significance
PPE35 2170461 p.Gly51Glu missense_variant 0.43 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.27 bedaquiline Not assoc w R - Interim
clofazimine 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 0.4 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.52 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.34 isoniazid
eis 2714526 c.805_806delAC frameshift_variant 0.12 kanamycin Uncertain significance
amikacin Uncertain significance
ahpC 2726051 c.-142G>A upstream_gene_variant 0.36 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.47 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.42 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 2996876 c.138A>C synonymous_variant 0.17 capreomycin Not assoc w R
Rv2681 2996912 c.174C>T synonymous_variant 0.38 capreomycin Not assoc w R
Rv2752c 3064532 p.Thr554Ala missense_variant 0.11 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3064632 c.1560C>T synonymous_variant 0.32 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
Rv2752c 3064674 c.1518C>T synonymous_variant 0.12 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086788 c.-32T>C upstream_gene_variant 0.91 cycloserine
ald 3087052 p.Ile78Thr missense_variant 0.2 cycloserine
fbiD 3339741 c.624G>A synonymous_variant 0.15 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
Rv3083 3448714 p.Asp71His missense_variant 0.22 ethionamide Uncertain significance
whiB7 3569029 c.-350A>G upstream_gene_variant 0.11 kanamycin Not assoc w R
amikacin Uncertain significance
streptomycin Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.1 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.34 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3625039 c.-129C>G upstream_gene_variant 0.16 rifampicin
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 0.94 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626290 c.324C>G synonymous_variant 0.13 rifampicin
bedaquiline
mtrA 3626907 p.Asn148Ser missense_variant 0.1 rifampicin Uncertain significance
bedaquiline
clpC1 4040517 p.Val63Ala missense_variant 0.34 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.39 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.23 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4138622 c.1134C>T synonymous_variant 0.41 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 0.15 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.24 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.27 ethambutol Not assoc w R
embC 4241562 p.Arg567His missense_variant 0.21 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.39 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 0.15 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.33 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.22 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.24 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.23 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.29 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.33 ethambutol Not assoc w R
ethA 4327629 c.-156C>T upstream_gene_variant 0.23 ethionamide
ethA 4328209 c.-736C>A upstream_gene_variant 0.11 ethionamide
ethA 4328329 c.-856C>G upstream_gene_variant 0.16 ethionamide
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 0.25 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 0.26 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.82 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.33 streptomycin Not assoc w R
gid 4407935 p.Leu90Val missense_variant 0.15 streptomycin Uncertain significance
gid 4407944 p.Gln87Glu missense_variant 0.15 streptomycin Uncertain significance