TB-Profiler result

Run: SRR26937050
Summary

Run ID: SRR26937050

Sample name:

Date: 2024-10-05T02:41:01.121994

Number of reads: 2700287

Percentage reads mapped: 98.97

Median coverage: 96.0

Strain: lineage1.1.1.1;lineage2.2.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.35
lineage1.1 Indo-Oceanic RD239 0.67
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.37
lineage2.2 East-Asian (Beijing) RD105;RD207 0.33
lineage1 Indo-Oceanic RD239 0.65
lineage1.1.1 Indo-Oceanic RD239 0.66
lineage1.1.1.1 Indo-Oceanic RD239 0.65
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide pncA c.380_389delAGGTCGATGT Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
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
rpsL 781687 p.Lys43Arg missense_variant 0.35 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.18 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.39 isoniazid Assoc w R High-level resistance
pncA 2288852 c.380_389delAGGTCGATGT frameshift_variant 0.31 pyrazinamide 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
gyrB 6112 p.Met291Ile missense_variant 0.69 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 0.68 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.67 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
gyrA 9368 c.2067G>A synonymous_variant 0.29 levofloxacin
moxifloxacin
Rv0010c 13275 p.Tyr95Cys missense_variant 0.6 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.65 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.56 isoniazid Not assoc w R
fgd1 490972 p.Arg64Ser missense_variant 0.65 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
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 0.41 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.43 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.29 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.27 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.69 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.68 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 0.57 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.56 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.59 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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.4 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 777581 p.Tyr300* stop_gained 0.62 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.24 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 0.66 linezolid Not assoc w R
Rv1129c 1254543 c.-9T>G upstream_gene_variant 0.67 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin 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 0.47 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.55 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.76 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.66 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.31 pyrazinamide Not assoc w R - Interim
rpsA 1834319 p.Val260Ile missense_variant 0.68 pyrazinamide Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.6 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.58 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 0.53 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063106 c.1623G>A synonymous_variant 0.7 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.99 isoniazid Not assoc w R
katG 2156389 c.-278G>C upstream_gene_variant 0.62 isoniazid Not assoc w R
katG 2156481 c.-370G>A upstream_gene_variant 0.61 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.67 pyrazinamide Uncertain significance
PPE35 2168548 p.Thr689Ala missense_variant 0.54 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.69 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
kasA 2518132 c.18C>T synonymous_variant 0.71 isoniazid
eis 2714526 c.805_806delAC frameshift_variant 0.4 kanamycin Uncertain significance
amikacin Uncertain significance
ahpC 2726051 c.-142G>A upstream_gene_variant 0.64 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.56 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 3065711 p.Gly161Ser missense_variant 0.36 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 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.6 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.28 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.75 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 3626562 p.Pro18Ser missense_variant 0.42 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.75 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.67 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 4139074 p.Leu228Val missense_variant 0.76 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
streptomycin Uncertain significance
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.64 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.58 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 0.46 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.57 ethambutol Not assoc w R
embA 4244096 c.864C>T synonymous_variant 0.66 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.63 ethambutol Not assoc w R
embB 4246660 c.147C>T synonymous_variant 0.39 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 0.66 ethambutol Not assoc w R
embB 4248320 p.Gly603Arg missense_variant 0.63 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.36 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.63 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.68 ethambutol Not assoc w R
whiB6 4338242 p.Gln94Glu missense_variant 0.59 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 0.66 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 0.64 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.36 streptomycin Not assoc w R
gid 4407982 p.Leu74Ser missense_variant 0.6 streptomycin Uncertain significance