Run ID: ERR4815985
Sample name:
Date: 2024-10-04T05:23:48.709875
Number of reads: 3194047
Percentage reads mapped: 95.05
Median coverage: 72.0
Strain: lineage5.1.2
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage5.1.2 | West-Africa 1 | RD711 | 1.0 |
lineage5 | West-Africa 1 | RD711 | 1.0 |
lineage5.1 | West-Africa 1 | RD711 | 0.87 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | rrs | n.888G>A | Uncertain significance | Mutation from literature |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.14 | streptomycin | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1125 | c.1125G>A | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
gyrB | 6446 | p.Ala403Ser | missense_variant | 1.0 | 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 | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
Rv0010c | 13460 | c.99T>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
Rv0010c | 13579 | c.-21G>A | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 1.0 | ethionamide | |
hadA | 731750 | c.-180G>C | upstream_gene_variant | 1.0 | isoniazid | |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Uncertain significance | |||||
Rv1258c | 1407273 | p.Asp23Val | missense_variant | 1.0 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472210 | n.365A>T | non_coding_transcript_exon_variant | 0.32 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.31 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.3 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.32 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.34 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472251 | n.406G>T | non_coding_transcript_exon_variant | 0.3 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472252 | n.407G>C | non_coding_transcript_exon_variant | 0.24 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472253 | n.408G>T | non_coding_transcript_exon_variant | 0.24 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472256 | n.411T>A | non_coding_transcript_exon_variant | 0.24 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 0.26 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472734 | n.889C>T | non_coding_transcript_exon_variant | 0.41 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472741 | n.896G>A | non_coding_transcript_exon_variant | 0.42 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.56 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.14 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472767 | n.922G>A | non_coding_transcript_exon_variant | 0.52 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.67 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472785 | n.940G>T | non_coding_transcript_exon_variant | 0.51 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472786 | n.941C>G | non_coding_transcript_exon_variant | 0.51 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472827 | n.982G>T | non_coding_transcript_exon_variant | 0.27 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473038 | n.1193A>C | non_coding_transcript_exon_variant | 0.26 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.25 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473053 | n.1208T>A | non_coding_transcript_exon_variant | 0.28 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473068 | n.1223A>G | non_coding_transcript_exon_variant | 0.34 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473070 | n.1225G>C | non_coding_transcript_exon_variant | 0.34 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473071 | n.1226C>A | non_coding_transcript_exon_variant | 0.36 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473080 | n.1235C>T | non_coding_transcript_exon_variant | 0.37 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473088 | n.1243A>G | non_coding_transcript_exon_variant | 0.34 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473093 | n.1248C>T | non_coding_transcript_exon_variant | 0.17 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
inhA | 1673338 | c.-864G>A | upstream_gene_variant | 1.0 | isoniazid | |
ethionamide | ||||||
tsnR | 1853565 | c.-41G>A | upstream_gene_variant | 1.0 | linezolid | Uncertain significance |
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 | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
ndh | 2101921 | c.1122G>A | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
delamanid | Not assoc w R - Interim | |||||
ethionamide | Not assoc w R - Interim | |||||
ndh | 2103112 | c.-70G>T | upstream_gene_variant | 1.0 | isoniazid | Not assoc w R - Interim |
delamanid | Uncertain significance | |||||
ethionamide | Uncertain significance | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
PPE35 | 2170265 | c.347delG | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
pncA | 2290062 | c.-821G>A | upstream_gene_variant | 1.0 | pyrazinamide | |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
ahpC | 2726261 | c.69G>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
ald | 3087084 | c.266delA | frameshift_variant | 1.0 | cycloserine | |
ald | 3087184 | c.368_373delCCGACG | disruptive_inframe_deletion | 1.0 | cycloserine | |
Rv3083 | 3449644 | p.Ala381Thr | missense_variant | 1.0 | ethionamide | Uncertain significance |
lpqB | 3624350 | c.561G>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
lpqB | 3624486 | p.Asp142Gly | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
alr | 3840932 | c.489C>T | synonymous_variant | 1.0 | cycloserine | |
rpoA | 3878493 | c.15G>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
ddn | 3986987 | c.144G>T | synonymous_variant | 1.0 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
ddn | 3987180 | p.Asp113Asn | missense_variant | 1.0 | pretomanid | |
delamanid | Uncertain significance | |||||
clpC1 | 4040824 | c.-120C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
glpK | 4138377 | p.Val460Ala | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
glpK | 4139131 | p.Glu209Lys | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Uncertain significance | |||||
embC | 4239843 | c.-20A>C | upstream_gene_variant | 1.0 | ethambutol | Not assoc w R - Interim |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | 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 | 1.0 | ethambutol | Not assoc w R |
embA | 4244635 | p.Val468Ala | missense_variant | 1.0 | ethambutol | Not assoc w R - Interim |
embA | 4245147 | p.Pro639Ser | missense_variant | 1.0 | ethambutol | Not assoc w R - Interim |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4249744 | c.3231G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4326928 | c.546C>T | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
ethA | 4327103 | p.Gly124Asp | missense_variant | 1.0 | ethionamide | Uncertain significance |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |