TB-Profiler result

Run: ERR702427
Summary

Run ID: ERR702427

Sample name:

Date: 2024-04-15T07:13:09.743912

Number of reads: 4066982

Percentage reads mapped: 99.44

Median coverage: 86.0

Strain: lineage4.6.2.2;lineage6

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 0.75
lineage4.6.2 Euro-American RD726 0.75
lineage4.6.2.2 Euro-American (Cameroon) RD726 0.74
lineage4 Euro-American None 0.73
lineage6 West-Africa 2 RD702 0.22
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
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
katG 2155168 p.Ser315Thr missense_variant 0.38 isoniazid Assoc w R High-level resistance
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 0.16 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrA 6580 c.-722C>A upstream_gene_variant 0.27 levofloxacin
moxifloxacin
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 8493 p.Leu398Phe missense_variant 0.17 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9143 c.1842T>C synonymous_variant 0.2 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 13460 c.99T>C synonymous_variant 0.2 isoniazid Not assoc w R
fgd1 491668 p.Lys296Glu missense_variant 0.25 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.28 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 656432 p.Gly347Ser missense_variant 0.25 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.24 ethionamide
rpoB 760969 p.Ser388Leu missense_variant 0.35 rifampicin Not assoc w R
rpoB 761723 p.Glu639Asp missense_variant 0.3 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.29 rifampicin Not assoc w R
rpoC 766231 c.2862T>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
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 0.21 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 778298 c.183G>A synonymous_variant 0.8 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253636 p.Arg300His missense_variant 0.35 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.21 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 0.31 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fbiC 1303216 p.Arg96Trp missense_variant 0.41 clofazimine
pretomanid
delamanid
Rv1258c 1406685 p.Val219Ala missense_variant 0.32 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1416633 p.Leu239Val missense_variant 0.25 ethambutol Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.26 ethambutol
atpE 1461251 c.207G>T synonymous_variant 0.22 bedaquiline Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1674434 p.Val78Ala missense_variant 0.32 ethionamide Uncertain significance
isoniazid 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 0.25 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 0.22 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
bacA 2063187 c.1542C>T synonymous_variant 0.8 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ndh 2102162 p.Arg294Gln missense_variant 0.33 ethionamide Uncertain significance
delamanid
isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.35 isoniazid Not assoc w R
katG 2155389 c.723C>G synonymous_variant 0.12 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.23 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.25 pyrazinamide Not assoc w R
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.71 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.16 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 2289037 p.Pro69Ser missense_variant 0.21 pyrazinamide Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 0.23 isoniazid
Rv2680 2996208 p.Ala35Asp missense_variant 0.74 capreomycin Uncertain significance
Rv2752c 3064864 p.Pro443Leu missense_variant 0.34 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
thyX 3067474 p.Pro158Ala missense_variant 0.76 para-aminosalicylic_acid
ald 3086728 c.-92C>T upstream_gene_variant 0.14 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.28 cycloserine
ald 3087084 c.266delA frameshift_variant 0.16 cycloserine
Rv3083 3448567 p.His22Asp missense_variant 0.74 ethionamide Uncertain significance
whiB7 3569082 c.-403G>A upstream_gene_variant 0.26 streptomycin
amikacin
kanamycin
Rv3236c 3612143 p.Arg325His missense_variant 0.24 pyrazinamide Uncertain significance
Rv3236c 3612571 c.546C>T synonymous_variant 0.81 pyrazinamide Not assoc w R
lpqB 3624350 c.561G>T synonymous_variant 0.22 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.25 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.29 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626238 p.Ala126Pro missense_variant 0.18 bedaquiline
rifampicin
glpK 4138377 p.Val460Ala missense_variant 0.23 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
embC 4240671 p.Thr270Ile missense_variant 0.29 ethambutol Not assoc w R
embC 4241843 p.Leu661Ile missense_variant 0.25 ethambutol Not assoc w R
embC 4242550 c.2688C>G synonymous_variant 0.74 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 0.25 ethambutol Not assoc w R
embA 4244379 p.Pro383Ser missense_variant 0.32 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 0.2 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.22 ethambutol Not assoc w R
aftB 4267272 p.Lys522Arg missense_variant 0.83 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 0.24 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.2 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.27 ethambutol Not assoc w R
ubiA 4269955 c.-122T>C upstream_gene_variant 0.19 ethambutol
ethA 4326465 p.Ile337Val missense_variant 0.23 ethionamide Uncertain significance
ethA 4326739 c.735C>G synonymous_variant 0.84 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 0.9 ethionamide Not assoc w R - Interim
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 0.26 streptomycin Not assoc w R
gid 4407973 p.Val77Gly missense_variant 0.53 streptomycin Uncertain significance
gid 4408034 p.Glu57Lys missense_variant 0.26 streptomycin Uncertain significance