TB-Profiler result

Run: ERR9786448
Summary

Run ID: ERR9786448

Sample name:

Date: 2024-04-15T12:05:34.739836

Number of reads: 1144287

Percentage reads mapped: 99.71

Median coverage: 47.0

Strain: lineage4.7;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 0.22
lineage4.7 Euro-American (mainly T) None 0.76
lineage4 Euro-American None 0.76
lineage6.3.1 West-Africa 2 RD702 0.25
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
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 0.3 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrB 6798 p.Gly520Ala missense_variant 0.79 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 9143 c.1842T>C synonymous_variant 0.14 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491668 p.Lys296Glu missense_variant 0.18 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
mshA 575578 c.231G>C synonymous_variant 0.64 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ccsA 619628 c.-263G>A upstream_gene_variant 0.27 capreomycin
amikacin
kanamycin
Rv0565c 656432 p.Gly347Ser missense_variant 0.25 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.34 ethionamide
nusG 734151 c.-103G>C upstream_gene_variant 0.25 rifampicin Uncertain significance
rpoB 760969 p.Ser388Leu missense_variant 0.41 rifampicin Not assoc w R
rpoB 761723 p.Glu639Asp missense_variant 0.23 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.23 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.17 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 0.22 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv1258c 1406363 c.978A>G synonymous_variant 0.24 streptomycin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
pyrazinamide Not assoc w R - Interim
embR 1417554 c.-207C>G upstream_gene_variant 0.31 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.76 capreomycin Not assoc w R
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.21 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 0.27 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 2102022 p.Lys341Glu missense_variant 0.25 ethionamide
delamanid
isoniazid Uncertain significance
ndh 2102694 p.Val117Ile missense_variant 0.26 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.24 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.27 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.31 pyrazinamide Not assoc w R
Rv1979c 2222852 p.Ala105Thr missense_variant 0.34 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 0.22 isoniazid
ald 3086728 c.-92C>T upstream_gene_variant 0.19 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.25 cycloserine
ald 3086958 p.Asp47Tyr missense_variant 0.26 cycloserine
ald 3087084 c.266delA frameshift_variant 0.28 cycloserine
Rv3083 3449781 c.1278G>A synonymous_variant 0.17 ethionamide Not assoc w R - Interim
Rv3236c 3613354 c.-238G>T upstream_gene_variant 0.23 pyrazinamide
lpqB 3624486 p.Asp142Gly missense_variant 0.34 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.29 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3877696 p.Thr271Ile missense_variant 0.25 rifampicin Uncertain significance
clpC1 4040489 c.216G>A synonymous_variant 0.28 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.33 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 0.4 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 0.27 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.25 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 0.92 ethambutol Not assoc w R
aftB 4267992 p.Thr282Met missense_variant 0.73 ethambutol Uncertain significance
ubiA 4269351 c.483C>T synonymous_variant 0.2 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.22 ethambutol Not assoc w R
ubiA 4269522 c.312C>T synonymous_variant 0.2 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.27 ethambutol Not assoc w R
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 0.45 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.25 streptomycin Not assoc w R