TB-Profiler result

Run: ERR4799915
Summary

Run ID: ERR4799915

Sample name:

Date: 2024-04-15T01:59:53.403065

Number of reads: 3836078

Percentage reads mapped: 99.45

Median coverage: 100.0

Strain: lineage1.2.2.2;lineage4

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2 Indo-Oceanic RD239 0.47
lineage1.2.2.2 Indo-Oceanic RD239 0.47
lineage4 Euro-American None 0.51
lineage1 Indo-Oceanic RD239 0.45
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 gid p.Ser136* 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
gid 4407796 p.Ser136* stop_gained 0.12 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 5075 c.-165C>T upstream_gene_variant 0.44 levofloxacin
moxifloxacin
gyrB 5115 c.-125G>T upstream_gene_variant 0.47 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.55 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.69 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 0.49 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8945 c.1644G>A synonymous_variant 0.45 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9143 c.1842T>C synonymous_variant 0.52 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 0.52 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 0.5 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.42 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.59 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 656932 p.Gly180Asp missense_variant 0.34 ethionamide
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.49 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.57 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.53 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.43 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.42 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 0.48 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800343 c.-466G>A upstream_gene_variant 0.41 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.57 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.51 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.45 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.45 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.61 ethambutol
embR 1417978 c.-631G>A upstream_gene_variant 0.54 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.44 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.4 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 2064795 c.-67G>C upstream_gene_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
ndh 2102240 p.Arg268His missense_variant 0.47 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.57 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.57 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.52 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.57 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
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.52 clofazimine Not assoc w R
bedaquiline Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 0.5 isoniazid
eis 2714581 p.Ala251Gly missense_variant 0.56 amikacin Uncertain significance
kanamycin Uncertain significance
ahpC 2726051 c.-142G>A upstream_gene_variant 0.41 isoniazid
ahpC 2726418 p.Glu76Lys missense_variant 0.58 isoniazid Uncertain significance
folC 2747116 c.483G>A synonymous_variant 0.54 para-aminosalicylic_acid
Rv2681 2997200 c.462G>A synonymous_variant 0.47 capreomycin Not assoc w R - Interim
Rv2752c 3065883 c.309C>T synonymous_variant 0.38 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 0.58 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.62 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.48 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3624565 p.Leu116Phe missense_variant 0.45 bedaquiline
rifampicin
mtrB 3625065 p.Met517Leu missense_variant 0.49 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.43 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.57 pyrazinamide Not assoc w R - Interim
clpC1 4040719 c.-15A>G upstream_gene_variant 0.52 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.38 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 4139870 c.-115T>C upstream_gene_variant 0.41 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4240671 p.Thr270Ile missense_variant 0.36 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.37 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.37 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.38 ethambutol Not assoc w R
embB 4249195 c.2682C>T synonymous_variant 0.63 ethambutol Not assoc w R - Interim
aftB 4267344 p.Val498Ala missense_variant 0.53 ethambutol
aftB 4267960 p.Val293Met missense_variant 0.42 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.6 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.36 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.59 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.53 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.53 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
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 0.99 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.51 streptomycin Not assoc w R
gid 4407775 p.Asp143Ala missense_variant 0.24 streptomycin Uncertain significance
gid 4407848 p.Ala119Thr missense_variant 0.43 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.46 streptomycin Not assoc w R