TB-Profiler result

Run: SRR26159062
Summary

Run ID: SRR26159062

Sample name:

Date: 2024-10-04T03:00:54.995992

Number of reads: 1030283

Percentage reads mapped: 99.02

Median coverage: 21.0

Strain:

Spoligotype:

Drug-resistance: MDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2.2 Indo-Oceanic RD239 0.51
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.48
lineage1 Indo-Oceanic RD239 0.55
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.37
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
p.Ile491Phe Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
gid c.273_305delAGAACCGCTACTGCGCCGCACCGAGTTTCTTCGinsC 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
rpoB 761155 p.Ser450Leu missense_variant 0.37 rifampicin Assoc w R
rpoB 761277 p.Ile491Phe missense_variant 0.48 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.58 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.58 isoniazid Assoc w R High-level resistance
gid 4407898 c.273_305delAGAACCGCTACTGCGCCGCACCGAGTTTCTTCGinsC frameshift_variant&missense_variant 0.57 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
gyrB 6112 p.Met291Ile missense_variant 0.6 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 9143 c.1842T>C synonymous_variant 0.33 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 0.44 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.43 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.48 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.29 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
ccsA 620625 p.Ile245Met missense_variant 0.4 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.52 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.64 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.65 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.44 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 0.31 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.33 rifampicin Not assoc w R
rpoC 766809 p.Val1147Ala missense_variant 0.25 rifampicin Uncertain significance
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 0.58 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.61 bedaquiline
clofazimine
rpsL 781301 c.-259C>T upstream_gene_variant 0.5 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.53 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
embR 1417019 p.Cys110Tyr missense_variant 0.52 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.55 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.31 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.35 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.52 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 0.56 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
ndh 2103137 c.-95A>G upstream_gene_variant 0.44 isoniazid Uncertain significance
delamanid Uncertain significance
ethionamide Uncertain significance
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 0.52 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.44 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 0.52 bedaquiline Uncertain significance
clofazimine Not assoc w R
pncA 2289910 c.-669C>T upstream_gene_variant 0.61 pyrazinamide
ahpC 2726051 c.-142G>A upstream_gene_variant 0.31 isoniazid
Rv2752c 3064889 p.Lys435Glu missense_variant 0.43 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.7 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.5 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.63 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 0.54 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.47 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3641404 p.Trp288Arg missense_variant 0.29 pretomanid
delamanid
clofazimine
clpC1 4040517 p.Val63Ala missense_variant 0.47 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.59 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 4241042 p.Asn394Asp missense_variant 0.57 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 0.45 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.62 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.35 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.82 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.47 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.62 ethambutol Not assoc w R
ethA 4326439 p.Asn345Lys missense_variant 0.27 ethionamide 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 4338635 c.-114A>C upstream_gene_variant 0.61 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 0.59 streptomycin Not assoc w R
gid 4407898 p.Glu92Asp missense_variant 0.43 streptomycin Not assoc w R