TB-Profiler result

Run: SRR7516454
Summary

Run ID: SRR7516454

Sample name:

Date: 2024-04-15T20:22:16.868476

Number of reads: 4337424

Percentage reads mapped: 99.4

Median coverage: 130.0

Strain: lineage1.1.1.1;lineage2.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.47
lineage1.1 Indo-Oceanic RD239 0.49
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.51
lineage1 Indo-Oceanic RD239 0.52
lineage1.1.1 Indo-Oceanic RD239 0.52
lineage1.1.1.1 Indo-Oceanic RD239 0.53
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
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Val180Ala Assoc w R
streptomycin rpsL p.Lys43Arg 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 0.57 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.51 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288703 p.Val180Ala missense_variant 0.55 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.58 ethambutol 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 0.57 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 0.99 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 7634 c.333C>T synonymous_variant 0.53 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8452 p.Ala384Val missense_variant 0.43 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.48 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 13275 p.Tyr95Cys missense_variant 0.59 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.6 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.56 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.53 isoniazid Not assoc w R
fgd1 490972 p.Arg64Ser missense_variant 0.55 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.57 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.49 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.41 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.4 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.56 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.46 rifampicin Not assoc w R
rpoB 761998 p.Leu731Pro missense_variant 0.44 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.44 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.45 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.43 rifampicin Not assoc w R
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 776182 p.Asp767Asn missense_variant 0.48 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 777581 p.Tyr300* stop_gained 0.45 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.51 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.41 linezolid Not assoc w R
Rv1129c 1253395 c.1140C>T synonymous_variant 0.47 moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv1129c 1254543 c.-9T>G upstream_gene_variant 0.41 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid 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
Rv1258c 1406760 c.580_581insC frameshift_variant 0.46 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.54 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.45 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.45 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.49 pyrazinamide Not assoc w R - Interim
rpsA 1834319 p.Val260Ile missense_variant 0.5 pyrazinamide Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.52 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.5 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 0.51 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063106 c.1623G>A synonymous_variant 0.55 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2156389 c.-278G>C upstream_gene_variant 0.52 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.99 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.61 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.42 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 0.51 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.48 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.47 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
ald 3086731 c.-89A>G upstream_gene_variant 0.46 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.47 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.43 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.42 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 3626562 p.Pro18Ser missense_variant 0.37 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878647 c.-140G>C upstream_gene_variant 0.72 rifampicin Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.57 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.61 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
glpK 4139074 p.Leu228Val missense_variant 0.5 ethambutol Not assoc w R
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.47 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.53 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 0.52 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.53 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.55 ethambutol Not assoc w R
embA 4244096 c.864C>T synonymous_variant 0.58 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.54 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.48 ethambutol Not assoc w R
embB 4249384 c.2871G>A synonymous_variant 0.56 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.42 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.56 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.48 ethambutol Not assoc w R
ethR 4328005 p.Ile153Val missense_variant 0.5 ethionamide Uncertain significance
whiB6 4338242 p.Gln94Glu missense_variant 0.52 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338371 p.Thr51Pro missense_variant 0.51 capreomycin Not assoc w R
amikacin Not assoc w R
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 0.51 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 4407873 c.330G>T synonymous_variant 0.5 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.51 streptomycin Not assoc w R