TB-Profiler result

Run: SRR19576437
Summary

Run ID: SRR19576437

Sample name:

Date: 2024-10-05T14:26:40.969794

Number of reads: 9681909

Percentage reads mapped: 95.88

Median coverage: 120.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.2
lineage1.2.2.2 Indo-Oceanic RD239 0.79
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.2
lineage2.2 East-Asian (Beijing) RD105;RD207 0.26
lineage1 Indo-Oceanic RD239 0.94
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 5075 c.-165C>T upstream_gene_variant 0.63 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.91 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.75 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 7532 c.231T>C synonymous_variant 0.84 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.67 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.55 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.82 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.82 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.83 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.81 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.44 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.41 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 656107 c.1363dupA frameshift_variant 0.2 ethionamide Uncertain significance
Rv0565c 656180 p.Asp431Asn missense_variant 0.88 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.29 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.31 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.72 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.72 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.81 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.82 rifampicin Not assoc w R
rpoC 764426 p.Arg353Gly missense_variant 0.22 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 0.98 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpR5 778445 c.-545G>A upstream_gene_variant 0.54 bedaquiline
clofazimine
mmpS5 779615 c.-710C>G upstream_gene_variant 0.67 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.48 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 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 0.14 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1416506 p.Thr281Ile missense_variant 0.3 ethambutol
embR 1417019 p.Cys110Tyr missense_variant 0.86 ethambutol Not assoc w R
embR 1417197 p.Gly51Arg missense_variant 0.15 ethambutol Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.76 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.81 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.85 linezolid Not assoc w R
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 0.72 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063464 p.Ser422Asn missense_variant 0.29 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
bacA 2064135 c.594G>A synonymous_variant 0.18 kanamycin
capreomycin
streptomycin
amikacin
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.75 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.79 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
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.79 bedaquiline Uncertain significance
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.96 isoniazid
kasA 2519168 p.Ala352Pro missense_variant 0.17 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.82 isoniazid
Rv2477c 2782494 p.Asp517Asn missense_variant 0.31 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
Rv2477c 2783345 p.Arg233Pro missense_variant 0.23 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2680 2996604 p.Glu167Gly missense_variant 0.65 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448572 c.69G>A synonymous_variant 0.13 ethionamide
Rv3083 3448714 p.Asp71His missense_variant 0.77 ethionamide Uncertain significance
whiB7 3568855 c.-176G>A upstream_gene_variant 0.42 kanamycin
amikacin
streptomycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.2 pyrazinamide Not assoc w R - Interim
lpqB 3623269 p.Ala548Thr missense_variant 0.14 rifampicin Uncertain significance
bedaquiline Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.93 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626467 c.147G>A synonymous_variant 0.53 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.48 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878817 c.-310T>A upstream_gene_variant 0.73 rifampicin Not assoc w R
ddn 3987050 c.207C>T synonymous_variant 0.19 pretomanid
delamanid
clpC1 4040517 p.Val63Ala missense_variant 0.87 pyrazinamide Not assoc w R - Interim
panD 4043983 p.Thr100Ile missense_variant 0.25 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.74 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
embC 4240671 p.Thr270Ile missense_variant 0.57 ethambutol Not assoc w R
embC 4240759 c.897C>T synonymous_variant 0.17 ethambutol
embC 4241042 p.Asn394Asp missense_variant 0.89 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244456 c.1224C>G synonymous_variant 0.7 ethambutol Not assoc w R - Interim
embA 4245824 c.2592G>A synonymous_variant 0.16 ethambutol Not assoc w R - Interim
embA 4245969 p.Pro913Ser missense_variant 0.94 ethambutol Not assoc w R
embB 4247091 p.Thr193Ser missense_variant 0.23 ethambutol
embB 4247568 p.Leu352Arg missense_variant 0.28 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.76 ethambutol Not assoc w R
embB 4249757 p.Thr1082Ala missense_variant 0.21 ethambutol Not assoc w R
ubiA 4269160 p.Ser225Leu missense_variant 0.15 ethambutol
ubiA 4269387 p.Glu149Asp missense_variant 0.74 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.93 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.71 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.8 ethionamide Uncertain significance
whiB6 4338194 p.Arg110Trp missense_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.91 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338551 c.-30G>T upstream_gene_variant 0.83 kanamycin
capreomycin
amikacin
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 0.87 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
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.75 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.21 streptomycin Not assoc w R