TB-Profiler result

Run: ERR751293
Summary

Run ID: ERR751293

Sample name:

Date: 2024-10-04T03:53:02.794283

Number of reads: 4631321

Percentage reads mapped: 98.91

Median coverage: 96.0

Strain: lineage5.1.2;lineage6.3.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage6.3 West-Africa 2 RD702 0.65
lineage5.1.2 West-Africa 1 RD711 0.24
lineage6.3.1 West-Africa 2 RD702 0.65
lineage5 West-Africa 1 RD711 0.4
lineage5.1 West-Africa 1 RD711 0.29
lineage6 West-Africa 2 RD702 0.66
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
gyrB 6446 p.Ala403Ser missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 0.99 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 0.33 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 13482 p.Ala26Val missense_variant 0.74 isoniazid Not assoc w R
Rv0010c 13579 c.-21G>A upstream_gene_variant 0.3 isoniazid Uncertain significance
fgd1 491668 p.Lys296Glu missense_variant 0.77 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 619628 c.-263G>A upstream_gene_variant 0.55 kanamycin
capreomycin
amikacin
Rv0565c 656432 p.Gly347Ser missense_variant 0.72 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
hadA 731750 c.-180G>C upstream_gene_variant 0.19 isoniazid
nusG 734151 c.-103G>C upstream_gene_variant 0.75 rifampicin Uncertain significance
rpoB 760969 p.Ser388Leu missense_variant 0.66 rifampicin Not assoc w R
rpoB 761723 p.Glu639Asp missense_variant 0.57 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin 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 1302899 c.-32A>G upstream_gene_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
Rv1258c 1407273 p.Asp23Val missense_variant 0.34 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
atpE 1461251 c.207G>T synonymous_variant 0.76 bedaquiline Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1673338 c.-864G>A upstream_gene_variant 0.39 isoniazid
ethionamide
inhA 1674434 p.Val78Ala missense_variant 0.62 isoniazid Not assoc w R
ethionamide Uncertain significance
tsnR 1853565 c.-41G>A upstream_gene_variant 0.49 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
tlyA 1918692 c.753G>A synonymous_variant 0.63 capreomycin
bacA 2062922 p.Ile603Val missense_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063121 c.1608A>T synonymous_variant 0.73 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ndh 2101921 c.1122G>A synonymous_variant 0.41 isoniazid Not assoc w R - Interim
delamanid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
ndh 2102694 p.Val117Ile missense_variant 0.74 isoniazid Uncertain significance
delamanid Uncertain significance
ethionamide Uncertain significance
ndh 2103112 c.-70G>T upstream_gene_variant 0.4 isoniazid Not assoc w R - Interim
delamanid Uncertain significance
ethionamide Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.65 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2170265 c.347delG frameshift_variant 0.25 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2222852 p.Ala105Thr missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2290062 c.-821G>A upstream_gene_variant 0.32 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
ahpC 2726261 c.69G>T synonymous_variant 0.15 isoniazid Not assoc w R - Interim
Rv2680 2996192 p.Val30Ile missense_variant 0.58 capreomycin
ald 3086728 c.-92C>T upstream_gene_variant 0.7 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.71 cycloserine
ald 3087084 c.266delA frameshift_variant 1.0 cycloserine
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 0.3 cycloserine
Rv3083 3449644 p.Ala381Thr missense_variant 0.27 ethionamide Uncertain significance
Rv3083 3449781 c.1278G>A synonymous_variant 0.64 ethionamide Not assoc w R - Interim
Rv3236c 3613354 c.-238G>T upstream_gene_variant 0.57 pyrazinamide
lpqB 3624350 c.561G>T synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840932 c.489C>T synonymous_variant 0.38 cycloserine
rpoA 3877696 p.Thr271Ile missense_variant 0.73 rifampicin Uncertain significance
rpoA 3878493 c.15G>A synonymous_variant 0.33 rifampicin Not assoc w R - Interim
ddn 3986987 c.144G>T synonymous_variant 0.25 pretomanid
delamanid Not assoc w R - Interim
ddn 3987180 p.Asp113Asn missense_variant 0.36 pretomanid
delamanid Uncertain significance
clpC1 4040824 c.-120C>T upstream_gene_variant 0.24 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 1.0 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 4139131 p.Glu209Lys missense_variant 0.32 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Not assoc w R
ethambutol Uncertain significance
embC 4239843 c.-20A>C upstream_gene_variant 0.37 ethambutol Not assoc w R - Interim
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4241843 p.Leu661Ile missense_variant 0.68 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 4244379 p.Pro383Ser missense_variant 0.62 ethambutol Not assoc w R
embA 4244635 p.Val468Ala missense_variant 0.38 ethambutol Not assoc w R - Interim
embA 4245147 p.Pro639Ser missense_variant 0.27 ethambutol Not assoc w R - Interim
embB 4246864 c.351C>T synonymous_variant 0.72 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
aftB 4268477 c.360C>T synonymous_variant 0.45 ethambutol Not assoc w R - Interim
ubiA 4269351 c.483C>T synonymous_variant 0.67 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269522 c.312C>T synonymous_variant 0.52 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326465 p.Ile337Val missense_variant 0.64 ethionamide Uncertain significance
ethA 4326928 c.546C>T synonymous_variant 0.38 ethionamide Not assoc w R - Interim
ethA 4327103 p.Gly124Asp missense_variant 0.3 ethionamide Uncertain significance
whiB6 4338547 c.-26A>G upstream_gene_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 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