TB-Profiler result

Run: SRR1181314
Summary

Run ID: SRR1181314

Sample name:

Date: 2024-10-04T04:03:40.458879

Number of reads: 5124713

Percentage reads mapped: 98.54

Median coverage: 121.0

Strain: lineage1.2.2.1;lineage4.1.2

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2.1 Indo-Oceanic RD239 0.49
lineage1.2.2 Indo-Oceanic RD239 0.46
lineage4.1 Euro-American None 0.5
lineage4.1.2 Euro-American None 0.52
lineage4 Euro-American None 0.54
lineage1 Indo-Oceanic RD239 0.43
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
dnaA 237 c.237G>A synonymous_variant 0.49 isoniazid Not assoc w R - Interim
gyrB 5075 c.-165C>T upstream_gene_variant 0.44 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.48 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7323 p.Pro8Ala missense_variant 0.57 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 0.49 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.53 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 0.5 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.32 isoniazid Not assoc w R
fgd1 491060 p.Met93Thr missense_variant 0.4 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 0.53 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.49 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 574643 c.-705C>G upstream_gene_variant 0.53 isoniazid
ethionamide
ccsA 620659 p.Arg257Cys missense_variant 0.41 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
Rv0565c 656832 c.639G>A synonymous_variant 0.52 ethionamide Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.53 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.51 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.54 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.55 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.52 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.48 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.5 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.53 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 0.45 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776659 p.Asp608Asn missense_variant 0.53 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.5 linezolid Not assoc w R
rplC 800899 p.Ala31Thr missense_variant 0.59 linezolid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.49 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 0.48 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.48 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.51 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471842 n.-4T>G upstream_gene_variant 0.46 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
tsnR 1853569 c.-37C>T upstream_gene_variant 0.54 linezolid Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.48 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 0.3 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2064817 c.-89G>C upstream_gene_variant 0.48 kanamycin
capreomycin
streptomycin
amikacin
katG 2154724 p.Arg463Leu missense_variant 0.43 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.46 pyrazinamide Not assoc w R
PPE35 2168501 p.Phe704Leu missense_variant 0.47 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.36 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 2518076 c.-39C>T upstream_gene_variant 0.52 isoniazid
kasA 2518132 c.18C>T synonymous_variant 0.5 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.48 isoniazid
thyX 3068115 c.-170C>T upstream_gene_variant 0.49 para-aminosalicylic_acid
thyA 3074034 c.438T>C synonymous_variant 0.48 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.55 ethionamide Uncertain significance
lpqB 3623539 p.Val458Leu missense_variant 0.27 rifampicin
bedaquiline
lpqB 3624486 p.Asp142Gly missense_variant 0.51 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 3625581 c.1033C>A synonymous_variant 0.48 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
rpoA 3878381 c.127C>T synonymous_variant 0.42 rifampicin Not assoc w R - Interim
clpC1 4040517 p.Val63Ala missense_variant 0.5 pyrazinamide Not assoc w R - Interim
clpC1 4040973 c.-269C>T upstream_gene_variant 0.54 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.4 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 0.5 ethambutol Not assoc w R
embC 4240750 c.888C>T synonymous_variant 0.53 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.52 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.65 ethambutol Not assoc w R
embA 4243290 p.Ser20Ala missense_variant 0.65 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.45 ethambutol Not assoc w R
embB 4247121 p.Ser203Leu missense_variant 0.62 ethambutol Uncertain significance
embB 4247646 p.Glu378Ala missense_variant 0.42 ethambutol Not assoc w R
aftB 4268852 c.-16G>A upstream_gene_variant 0.49 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.55 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.35 ethambutol Not assoc w R
ethA 4326439 p.Asn345Lys missense_variant 0.39 ethionamide Uncertain significance
ethA 4327450 c.24C>T synonymous_variant 0.46 ethionamide Not assoc w R - Interim
whiB6 4338215 p.Gly103Cys missense_variant 0.49 kanamycin
capreomycin
amikacin
whiB6 4338374 p.Lys50Glu missense_variant 0.53 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 0.49 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 0.46 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.45 streptomycin Not assoc w R
gid 4408397 c.-195A>G upstream_gene_variant 0.47 streptomycin