TB-Profiler result

Run: SRR25827630
Summary

Run ID: SRR25827630

Sample name:

Date: 2024-04-15T23:23:08.216143

Number of reads: 7120086

Percentage reads mapped: 98.98

Median coverage: 249.0

Strain: lineage1.1.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.2 Indo-Oceanic RD239 0.76
lineage1.1 Indo-Oceanic RD239 0.99
lineage1 Indo-Oceanic RD239 0.99
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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.74 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 1.0 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 1.0 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.99 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 576675 p.Arg443His missense_variant 0.23 ethionamide Uncertain significance
isoniazid Not assoc w R - Interim
Rv0565c 656269 p.Met401Thr missense_variant 0.76 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.78 rifampicin Not assoc w R
rpoB 759886 p.Pro27His missense_variant 0.21 rifampicin Uncertain significance
rpoB 760490 c.684C>T synonymous_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 0.98 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.98 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 1.0 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.23 rifampicin Not assoc w R
rpoC 767308 c.3939C>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776395 p.Phe696Leu missense_variant 0.74 clofazimine Not assoc w R
bedaquiline Uncertain significance
mmpL5 778099 p.Asp128Asn missense_variant 0.22 clofazimine Uncertain significance
bedaquiline 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 0.99 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364746 c.334C>T synonymous_variant 0.71 pyrazinamide Not assoc w R - Interim
Rv1258c 1407190 c.123_150delTGGGCAGGCCTCGATCGTGGCCAGTGCG frameshift_variant 0.18 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1416574 c.774A>G synonymous_variant 0.28 ethambutol Not assoc w R - Interim
embR 1417019 p.Cys110Tyr missense_variant 1.0 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 1.0 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 1.0 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 1.0 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.99 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.99 pyrazinamide Uncertain significance
PPE35 2170785 c.-173T>C upstream_gene_variant 0.68 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 0.99 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 0.99 isoniazid
kasA 2518173 p.Thr20Ile missense_variant 0.71 isoniazid
eis 2715016 p.Arg106His missense_variant 0.7 amikacin Uncertain significance
kanamycin Uncertain significance
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0 isoniazid
Rv2681 2996912 c.174C>T synonymous_variant 0.74 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv2752c 3065419 p.Arg258Leu missense_variant 0.7 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
ald 3086767 c.-53A>T upstream_gene_variant 0.24 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.99 ethionamide Uncertain significance
Rv3236c 3613309 c.-193G>A upstream_gene_variant 0.72 pyrazinamide
lpqB 3624486 p.Asp142Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.76 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
fbiA 3640320 c.-223G>T upstream_gene_variant 0.72 clofazimine
pretomanid
delamanid
alr 3840948 p.Val158Ala missense_variant 0.27 cycloserine
rpoA 3878575 c.-68C>A upstream_gene_variant 0.73 rifampicin Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.99 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.72 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4243056 p.Pro1065Leu missense_variant 0.23 ethambutol Uncertain significance
embA 4243848 p.Val206Met missense_variant 1.0 ethambutol Not assoc w R
embA 4245314 c.2082G>C synonymous_variant 0.26 ethambutol Not assoc w R - Interim
embA 4245969 p.Pro913Ser missense_variant 1.0 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.14 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.99 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.99 ethambutol Not assoc w R
ubiA 4269523 p.Thr104Ile missense_variant 0.76 ethambutol Uncertain significance
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338386 p.Asp46His missense_variant 0.81 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.99 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407780 c.423G>A synonymous_variant 0.24 streptomycin Not assoc w R - Interim
gid 4407873 c.330G>T synonymous_variant 0.99 streptomycin Not assoc w R
gid 4408252 c.-50A>G upstream_gene_variant 0.26 streptomycin Uncertain significance
gid 4408338 c.-136A>G upstream_gene_variant 0.3 streptomycin
gid 4408478 c.-276C>A upstream_gene_variant 0.27 streptomycin