TB-Profiler result

Run: ERR9786868
Summary

Run ID: ERR9786868

Sample name:

Date: 2024-04-16T00:26:45.923892

Number of reads: 2987498

Percentage reads mapped: 99.72

Median coverage: 149.0

Strain: lineage4.3.4.2;lineage6.1.3

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.77
lineage6.1.3 West-Africa 2 RD702 0.25
lineage4 Euro-American None 0.78
lineage4.3.4 Euro-American (LAM) RD174 0.78
lineage4.3.4.2 Euro-American (LAM) RD174 0.76
lineage6 West-Africa 2 RD702 0.25
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol embC p.Ala307Thr Uncertain significance Mutation from literature
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid fbiC c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.17 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
embC 4240781 p.Ala307Thr missense_variant 0.31 ethambutol Uncertain significance Mutation from literature
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 0.22 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrB 6817 c.1578G>A synonymous_variant 0.77 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
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 0.29 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8806 p.Asp502Gly missense_variant 0.25 levofloxacin
moxifloxacin
gyrA 9143 c.1842T>C synonymous_variant 0.18 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 13418 c.141G>A synonymous_variant 0.7 isoniazid Not assoc w R - Interim
Rv0010c 13460 c.99T>C synonymous_variant 0.3 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.28 isoniazid Not assoc w R
fgd1 491668 p.Lys296Glu missense_variant 0.17 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.25 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 656432 p.Gly347Ser missense_variant 0.21 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.3 ethionamide
rpoB 760855 p.Thr350Ile missense_variant 0.26 rifampicin Uncertain significance
rpoB 760969 p.Ser388Leu missense_variant 0.21 rifampicin Not assoc w R
rpoB 761723 p.Glu639Asp missense_variant 0.19 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.18 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.78 rifampicin Not assoc w R
rpoC 766231 c.2862T>C synonymous_variant 0.25 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 0.22 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
rplC 800232 c.-577G>T upstream_gene_variant 0.29 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.25 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 1406685 p.Val219Ala missense_variant 0.23 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 0.25 ethambutol
atpE 1461251 c.207G>T synonymous_variant 0.26 bedaquiline Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472912 n.1067C>T non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473633 n.-25C>T upstream_gene_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674434 p.Val78Ala missense_variant 0.23 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 0.2 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 0.25 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.28 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.27 isoniazid Not assoc w R
katG 2156815 c.-704A>G upstream_gene_variant 0.69 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 0.28 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.28 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
kasA 2518132 c.18C>T synonymous_variant 0.21 isoniazid
eis 2714432 p.Val301Ile missense_variant 0.8 amikacin Uncertain significance
kanamycin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.74 para-aminosalicylic_acid
ald 3086728 c.-92C>T upstream_gene_variant 0.23 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 0.22 cycloserine
ald 3087412 p.Asp198Val missense_variant 0.27 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.8 pyrazinamide Not assoc w R
Rv3236c 3612143 p.Arg325His missense_variant 0.18 pyrazinamide Uncertain significance
lpqB 3624350 c.561G>T synonymous_variant 0.29 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.32 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626184 p.Ala144Thr missense_variant 0.26 bedaquiline
rifampicin
rpoA 3877740 c.768G>C synonymous_variant 0.25 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 0.73 pyrazinamide Not assoc w R
glpK 4138377 p.Val460Ala missense_variant 0.21 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 4139183 c.572dupG frameshift_variant 0.12 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4239426 c.-437C>G upstream_gene_variant 0.27 ethambutol
embC 4239763 c.-100C>T upstream_gene_variant 0.76 ethambutol Not assoc w R
embC 4240382 p.Gly174Arg missense_variant 0.77 ethambutol Uncertain significance
embC 4240612 c.750C>T synonymous_variant 0.4 ethambutol
embC 4240671 p.Thr270Ile missense_variant 0.38 ethambutol Not assoc w R
embC 4241843 p.Leu661Ile missense_variant 0.26 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 0.22 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 0.32 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.2 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 0.26 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.28 ethambutol Not assoc w R
ubiA 4269522 c.312C>T synonymous_variant 0.3 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.28 ethambutol Not assoc w R
ethA 4326465 p.Ile337Val missense_variant 0.23 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 4338602 c.-81A>C upstream_gene_variant 0.18 capreomycin
amikacin
kanamycin
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.24 streptomycin Not assoc w R
gid 4407775 p.Asp143Gly missense_variant 0.26 streptomycin
gid 4408034 p.Glu57Lys missense_variant 0.22 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.82 streptomycin Not assoc w R