TB-Profiler result

Run: SRR998625
Summary

Run ID: SRR998625

Sample name:

Date: 2024-04-15T06:01:07.577621

Number of reads: 738490

Percentage reads mapped: 99.08

Median coverage: 16.0

Strain: lineage5.1.1;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 0.32
lineage5.1.1 West-Africa 1 RD711 0.59
lineage6.3.1 West-Africa 2 RD702 0.36
lineage5.1 West-Africa 1 RD711 0.33
lineage6 West-Africa 2 RD702 0.4
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 0.95 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 0.62 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13460 c.99T>C synonymous_variant 0.95 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.58 isoniazid Not assoc w R
Rv0010c 13579 c.-21G>A upstream_gene_variant 0.43 isoniazid Uncertain significance
fgd1 491668 p.Lys296Glu missense_variant 0.5 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.94 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 656432 p.Gly347Ser missense_variant 0.47 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.9 ethionamide
hadA 731750 c.-180G>C upstream_gene_variant 0.54 isoniazid
nusG 734151 c.-103G>C upstream_gene_variant 0.54 rifampicin Uncertain significance
rpoB 760969 p.Ser388Leu missense_variant 0.5 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763904 p.Ala179Ser missense_variant 0.47 rifampicin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.86 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 1406740 p.His201Tyr missense_variant 0.47 streptomycin
isoniazid
pyrazinamide
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 0.6 ethionamide
isoniazid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.86 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063121 c.1608A>T synonymous_variant 0.4 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ndh 2101921 c.1122G>A synonymous_variant 0.62 ethionamide Not assoc w R - Interim
delamanid Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ndh 2102694 p.Val117Ile missense_variant 0.56 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
ndh 2103112 c.-70G>T upstream_gene_variant 0.58 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.93 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.5 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2290062 c.-821G>A upstream_gene_variant 0.69 pyrazinamide
ald 3086728 c.-92C>T upstream_gene_variant 0.47 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.43 cycloserine
ald 3087084 c.266delA frameshift_variant 0.94 cycloserine
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 0.53 cycloserine
Rv3083 3449644 p.Ala381Thr missense_variant 0.5 ethionamide Uncertain significance
lpqB 3624350 c.561G>T synonymous_variant 0.95 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 0.93 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840932 c.489C>T synonymous_variant 0.53 cycloserine
rpoA 3878493 c.15G>A synonymous_variant 0.75 rifampicin Not assoc w R - Interim
ddn 3986987 c.144G>T synonymous_variant 0.58 delamanid Not assoc w R - Interim
pretomanid
ddn 3987180 p.Asp113Asn missense_variant 0.83 delamanid Uncertain significance
pretomanid
clpC1 4040010 p.Ala232Asp missense_variant 0.64 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.88 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 0.46 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4241843 p.Leu661Ile missense_variant 0.5 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 0.9 ethambutol Not assoc w R
aftB 4268477 c.360C>T synonymous_variant 0.65 ethambutol Not assoc w R - Interim
ubiA 4269351 c.483C>T synonymous_variant 0.38 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.93 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.88 ethambutol Not assoc w R
ethA 4326465 p.Ile337Val missense_variant 0.46 ethionamide 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