TB-Profiler result

Run: ERR161071
Summary

Run ID: ERR161071

Sample name:

Date: 2024-04-15T01:34:23.716094

Number of reads: 7198446

Percentage reads mapped: 99.38

Median coverage: 158.0

Strain: La1.1;lineage3

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
lineage3 East-African-Indian RD750 0.86
La1.1 M.bovis None 0.14
La1 M.bovis None 0.14
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 467 p.His156Arg missense_variant 0.14 isoniazid 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 8285 c.984C>T synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8660 c.1359C>T synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9143 c.1842T>C synonymous_variant 0.13 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 13197 p.Thr121Ser missense_variant 0.17 isoniazid Not assoc w R
Rv0010c 13228 c.330delG frameshift_variant 0.18 isoniazid Uncertain significance
Rv0010c 13460 c.99T>C synonymous_variant 0.11 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.99 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.81 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.14 ethionamide
rpoB 759746 c.-61C>T upstream_gene_variant 0.85 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.86 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 766582 c.3213C>A synonymous_variant 0.89 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 0.99 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 778066 p.Ala139Thr missense_variant 0.14 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781517 c.-43C>T upstream_gene_variant 0.13 streptomycin
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.99 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254582 c.-48A>G upstream_gene_variant 0.14 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.19 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.19 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472437 n.592T>G non_coding_transcript_exon_variant 0.13 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476704 n.3053dupC non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
fabG1 1673254 c.-186A>C upstream_gene_variant 0.1 ethionamide
isoniazid
rpsA 1834859 p.Ala440Thr missense_variant 0.14 pyrazinamide Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.99 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.21 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2103173 c.-132delG upstream_gene_variant 0.13 ethionamide
delamanid
isoniazid
katG 2154724 p.Arg463Leu missense_variant 0.99 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.14 isoniazid Not assoc w R
katG 2156025 c.87C>A synonymous_variant 0.14 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.99 pyrazinamide Not assoc w R
PPE35 2168011 p.Ser868Arg missense_variant 0.15 pyrazinamide Uncertain significance
PPE35 2168814 c.1798dupA frameshift_variant 0.13 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.13 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
pncA 2289047 c.195C>T synonymous_variant 0.81 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.88 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.15 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.81 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.86 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2477c 2782927 c.1116A>G synonymous_variant 0.13 ethambutol Not assoc w R
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R
amikacin Not assoc w R - Interim
Rv2680 2995899 c.-205delC upstream_gene_variant 0.2 capreomycin
Rv2681 2997325 p.Ala196Val missense_variant 0.15 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 0.15 cycloserine
Rv3083 3448783 p.Val94Ile missense_variant 0.15 ethionamide Uncertain significance
lpqB 3623730 p.Ser394Leu missense_variant 0.14 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3624350 c.561G>T synonymous_variant 0.11 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.15 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627711 c.-362C>A upstream_gene_variant 0.14 bedaquiline
rifampicin
alr 3841473 c.-53G>A upstream_gene_variant 0.87 cycloserine
alr 3841559 c.-139C>T upstream_gene_variant 0.86 cycloserine
rpoA 3878568 c.-61G>A upstream_gene_variant 0.15 rifampicin
clpC1 4038596 c.2109A>G synonymous_variant 0.12 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.89 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.13 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 4138622 c.1134C>T synonymous_variant 0.86 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.17 ethambutol Not assoc w R
embC 4241975 p.Gln705Glu missense_variant 0.2 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.86 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242970 c.3108C>T synonymous_variant 0.18 ethambutol Not assoc w R
embB 4247270 p.Leu253Ile missense_variant 0.81 ethambutol Uncertain significance
embB 4247646 p.Glu378Ala missense_variant 0.18 ethambutol Not assoc w R
embB 4249251 p.Ala913Val missense_variant 0.86 ethambutol
aftB 4267858 p.Ile327Val missense_variant 0.11 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 0.13 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.14 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.13 ethambutol Not assoc w R
whiB6 4338365 p.Cys53Arg missense_variant 0.82 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 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