TB-Profiler result

Run: SRR5065644
Summary

Run ID: SRR5065644

Sample name:

Date: 2024-10-03T16:30:51.434385

Number of reads: 2972840

Percentage reads mapped: 99.5

Median coverage: 92.0

Strain: lineage1.1.1.1;lineage2.2.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.91
lineage1.1 Indo-Oceanic RD239 0.06
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.9
lineage2.2 East-Asian (Beijing) RD105;RD207 0.88
lineage1 Indo-Oceanic RD239 0.07
lineage1.1.1 Indo-Oceanic RD239 0.09
lineage1.1.1.1 Indo-Oceanic RD239 0.09
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 rrs n.514A>C 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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.88 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
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.1 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
mshA 575907 p.Ala187Val missense_variant 0.93 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.88 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.9 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.88 ethionamide Uncertain significance
nusG 734116 c.-138T>C upstream_gene_variant 0.19 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 0.14 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.13 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 0.92 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.86 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254543 c.-9T>G upstream_gene_variant 0.13 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
fbiC 1304893 p.Gly655Ser missense_variant 0.86 pretomanid
delamanid
clofazimine
sigE 1365064 p.Leu218Val missense_variant 0.88 pyrazinamide
Rv1258c 1406760 c.580_581insC frameshift_variant 0.9 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.17 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.1 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.12 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.9 pyrazinamide Not assoc w R - Interim
rpsA 1834319 p.Val260Ile missense_variant 0.15 pyrazinamide Uncertain significance
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
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
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 0.16 isoniazid
eis 2714526 c.805_806delAC frameshift_variant 0.89 kanamycin Uncertain significance
amikacin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.82 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.15 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 0.86 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.19 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.11 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 0.15 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 4239722 c.-141C>T upstream_gene_variant 0.93 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.91 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.96 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.16 ethambutol Not assoc w R
ethA 4326166 c.1308A>G synonymous_variant 0.94 ethionamide
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 0.15 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 0.11 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.93 streptomycin Not assoc w R