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
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 | 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 |
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 |
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 |