TB-Profiler result

Run: ERR171164
Summary

Run ID: ERR171164

Sample name:

Date: 2024-10-03T23:38:46.462037

Number of reads: 2085809

Percentage reads mapped: 99.43

Median coverage: 43.0

Strain: lineage1.2.1.2.1;lineage4.4.2

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.1.2 Indo-Oceanic RD239 0.31
lineage4 Euro-American None 0.72
lineage1 Indo-Oceanic RD239 0.28
lineage1.2.1.2.1 Indo-Oceanic RD239 0.3
lineage1.2.1 Indo-Oceanic RD239 0.26
lineage4.4 Euro-American None 0.74
lineage4.4.2 Euro-American None 0.73
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.Glu24* 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 4408133 p.Glu24* stop_gained 0.29 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 6112 p.Met291Ile missense_variant 0.34 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 9143 c.1842T>C synonymous_variant 0.36 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9260 c.1959G>C synonymous_variant 0.32 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 13175 c.384T>C synonymous_variant 0.23 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.31 isoniazid Not assoc w R
fgd1 491377 p.Gly199Arg missense_variant 0.67 pretomanid
delamanid
clofazimine Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.38 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575368 c.21T>C synonymous_variant 0.24 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.27 ethionamide
rpoB 763031 c.3225T>C synonymous_variant 0.51 rifampicin Not assoc w R
rpoC 763531 c.162G>C synonymous_variant 0.38 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.37 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.35 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 0.25 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.31 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.27 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1407363 c.-23C>T upstream_gene_variant 0.39 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.43 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.31 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.22 ethambutol
atpE 1460907 c.-138T>C upstream_gene_variant 0.23 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1674162 c.-40C>T upstream_gene_variant 0.31 isoniazid Not assoc w R
ethionamide Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.27 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 0.35 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.3 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.32 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.25 bedaquiline Not assoc w R - Interim
clofazimine 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
pncA 2289524 c.-283C>T upstream_gene_variant 0.32 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.39 isoniazid
kasA 2519048 p.Gly312Ser missense_variant 0.26 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.26 isoniazid
Rv2752c 3066099 p.Met31Ile missense_variant 0.73 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339417 c.300A>G synonymous_variant 0.39 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
whiB7 3568488 c.191delG frameshift_variant 0.29 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.3 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640557 c.15T>C synonymous_variant 0.2 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
ddn 3987175 p.Ala111Val missense_variant 0.76 pretomanid
delamanid
clpC1 4040517 p.Val63Ala missense_variant 0.23 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.21 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
embC 4238963 c.-900C>T upstream_gene_variant 0.71 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.3 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.44 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243580 c.348G>A synonymous_variant 0.3 ethambutol Not assoc w R
embA 4244420 c.1188G>C synonymous_variant 0.24 ethambutol Not assoc w R
embA 4246508 c.3276G>A synonymous_variant 0.77 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.4 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 0.53 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.6 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.44 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.32 ethambutol Not assoc w R
ubiA 4269864 c.-32delG upstream_gene_variant 0.36 ethambutol Not assoc w R
ethA 4328200 c.-727C>T upstream_gene_variant 0.53 ethionamide
whiB6 4338361 p.Arg54Gln missense_variant 0.4 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
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 0.27 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 0.25 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.24 streptomycin Not assoc w R