TB-Profiler result

Run: ERR3170471
Summary

Run ID: ERR3170471

Sample name:

Date: 2024-06-18T11:40:07.081400

Number of reads: 1853081

Percentage reads mapped: 99.31

Median coverage: 54.0

Strain: lineage5.1.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage5.1.2 West-Africa 1 RD711 1.0
lineage5 West-Africa 1 RD711 1.0
lineage5.1 West-Africa 1 RD711 0.8
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Tyr Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gly406Ala Assoc w R
pyrazinamide
streptomycin rpsL p.Lys88Arg 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 761109 p.Asp435Tyr missense_variant 1.0 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embB 4247730 p.Gly406Ala missense_variant 1.0 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 6446 p.Ala403Ser missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
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 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
gyrA 9566 c.2265C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
Rv0010c 13579 c.-21G>A upstream_gene_variant 1.0 isoniazid Uncertain significance
fgd1 491216 p.Gly145Ala missense_variant 1.0 clofazimine
pretomanid
delamanid
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
hadA 731750 c.-180G>C upstream_gene_variant 1.0 isoniazid
rpoB 763031 c.3225T>C synonymous_variant 1.0 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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781415 c.-145C>T upstream_gene_variant 1.0 streptomycin
Rv1129c 1253759 p.Val259Ala missense_variant 1.0 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
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
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv1258c 1407273 p.Asp23Val missense_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
fabG1 1673338 c.-102G>A upstream_gene_variant 1.0 ethionamide
isoniazid
tsnR 1853565 c.-41G>A upstream_gene_variant 1.0 linezolid 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
bacA 2062922 p.Ile603Val missense_variant 1.0 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2101921 c.1122G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
delamanid Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ndh 2103112 c.-70G>T upstream_gene_variant 1.0 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R - Interim
ndh 2103217 c.-175C>T upstream_gene_variant 1.0 ethionamide
delamanid
isoniazid
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
PPE35 2170265 c.347delG frameshift_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2288742 p.Thr167Ile missense_variant 1.0 pyrazinamide Uncertain significance
pncA 2290062 c.-821G>A upstream_gene_variant 1.0 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
ahpC 2726261 c.69G>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
ald 3087084 c.266delA frameshift_variant 1.0 cycloserine
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 1.0 cycloserine
Rv3083 3449644 p.Ala381Thr missense_variant 1.0 ethionamide Uncertain significance
lpqB 3624350 c.561G>T synonymous_variant 1.0 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.98 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840932 c.489C>T synonymous_variant 1.0 cycloserine
rpoA 3878493 c.15G>A synonymous_variant 1.0 rifampicin Not assoc w R - Interim
ddn 3986987 c.144G>T synonymous_variant 1.0 delamanid Not assoc w R - Interim
pretomanid
ddn 3987180 p.Asp113Asn missense_variant 1.0 delamanid Uncertain significance
pretomanid
clpC1 4040824 c.-120C>T upstream_gene_variant 1.0 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 1.0 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 4139131 p.Glu209Lys missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Uncertain significance
embC 4239843 c.-20A>C upstream_gene_variant 1.0 ethambutol Not assoc w R - Interim
embC 4240671 p.Thr270Ile missense_variant 0.98 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244635 p.Val468Ala missense_variant 1.0 ethambutol Not assoc w R - Interim
embA 4245147 p.Pro639Ser missense_variant 1.0 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326110 p.Trp455Leu missense_variant 1.0 ethionamide
ethA 4326928 c.546C>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
ethA 4327103 p.Gly124Asp missense_variant 1.0 ethionamide Uncertain significance
ethA 4327540 c.-67C>T upstream_gene_variant 1.0 ethionamide
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