Run ID: ERR4872093
Sample name:
Date: 2024-04-16T12:40:34.738110
Number of reads: 4642657
Percentage reads mapped: 89.69
Median coverage: 129.0
Strain: lineage5.2
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage5.2 | West-Africa 1 | RD711 | 1.0 |
lineage5 | West-Africa 1 | RD711 | 0.98 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Gln432Lys | Assoc w R | |
p.His445Asp | Assoc w R | |||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embA | c.-29_-28delCT | Uncertain significance | Mutation from literature |
embB | p.Met306Ile | Assoc w R | ||
pyrazinamide | pncA | p.Gln10Pro | Assoc w R | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | fbiC | c.859_861delATCinsGG | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761100 | p.Gln432Lys | missense_variant | 0.93 | rifampicin | Assoc w R | |
rpoB | 761139 | p.His445Asp | missense_variant | 0.93 | rifampicin | Assoc w R | |
fbiC | 1303789 | c.859_861delATCinsGG | frameshift_variant&missense_variant | 0.14 | delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 0.93 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289213 | p.Gln10Pro | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
embA | 4243203 | c.-29_-28delCT | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance | Mutation from literature |
embB | 4247431 | p.Met306Ile | missense_variant | 0.95 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6446 | p.Ala403Ser | missense_variant | 0.97 | 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 | 0.99 | 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 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
ccsA | 619519 | c.-372C>T | upstream_gene_variant | 0.93 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 1.0 | ethionamide | |
Rv0565c | 657649 | c.-179G>A | upstream_gene_variant | 1.0 | ethionamide | |
hadA | 731750 | c.-180G>C | upstream_gene_variant | 0.99 | isoniazid | |
nusG | 734457 | c.204C>G | synonymous_variant | 0.14 | rifampicin | |
nusG | 734460 | c.207G>T | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
nusG | 734472 | c.219T>C | synonymous_variant | 0.16 | rifampicin | |
nusG | 734481 | c.228C>T | synonymous_variant | 0.16 | rifampicin | |
nusG | 734532 | c.279A>G | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoB | 760841 | c.1035T>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoB | 760845 | p.Thr347Ala | missense_variant | 0.14 | rifampicin | |
rpoB | 760859 | c.1053T>C | synonymous_variant | 0.14 | rifampicin | |
rpoB | 760862 | c.1056G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoB | 760925 | c.1119T>C | synonymous_variant | 0.15 | rifampicin | |
rpoB | 760928 | c.1122G>C | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoB | 760934 | c.1128C>T | synonymous_variant | 0.16 | rifampicin | |
rpoB | 760946 | c.1140A>G | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoB | 760982 | c.1176G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoB | 760985 | c.1179G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoB | 762131 | c.2325C>G | synonymous_variant | 0.15 | rifampicin | |
rpoB | 762140 | c.2334G>C | synonymous_variant | 0.14 | rifampicin | |
rpoB | 762143 | c.2337T>C | synonymous_variant | 0.14 | rifampicin | |
rpoB | 762149 | c.2343G>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 763702 | c.333C>G | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 763774 | c.405G>C | synonymous_variant | 0.14 | rifampicin | |
rpoC | 763792 | p.Glu141Asp | missense_variant | 0.14 | rifampicin | |
rpoC | 766864 | c.3495G>C | synonymous_variant | 0.13 | rifampicin | |
rpoC | 766894 | c.3525T>C | synonymous_variant | 0.15 | rifampicin | |
rpoC | 766900 | c.3531T>C | synonymous_variant | 0.15 | rifampicin | |
rpoC | 766933 | c.3564A>G | synonymous_variant | 0.16 | rifampicin | |
rpoC | 766945 | c.3576A>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 767011 | c.3642G>C | synonymous_variant | 0.13 | 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 | 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 |
rpsL | 781715 | c.156T>C | synonymous_variant | 0.15 | streptomycin | |
rpsL | 781728 | c.169T>C | synonymous_variant | 0.15 | streptomycin | |
rpsL | 781736 | c.177T>C | synonymous_variant | 0.14 | streptomycin | |
rpsL | 781742 | c.183C>T | synonymous_variant | 0.14 | streptomycin | |
rpsL | 781748 | c.189C>G | synonymous_variant | 0.16 | streptomycin | |
rpsL | 781754 | c.195G>T | synonymous_variant | 0.16 | streptomycin | |
rpsL | 781760 | c.201T>C | synonymous_variant | 0.17 | streptomycin | |
rpsL | 781772 | c.213C>T | synonymous_variant | 0.15 | streptomycin | Not assoc w R - Interim |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | 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 | 1.0 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
fbiC | 1303761 | c.831T>C | synonymous_variant | 0.14 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
fbiC | 1303785 | c.855G>C | synonymous_variant | 0.14 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
fbiC | 1303797 | c.867A>G | synonymous_variant | 0.16 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
fbiC | 1303818 | c.888C>G | synonymous_variant | 0.16 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
fbiC | 1303827 | c.897A>G | synonymous_variant | 0.14 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1476628 | n.2971T>A | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476689 | n.3032A>T | non_coding_transcript_exon_variant | 0.22 | capreomycin | |
linezolid | ||||||
rrl | 1476690 | n.3033C>T | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476693 | n.3036G>A | non_coding_transcript_exon_variant | 0.22 | capreomycin | |
linezolid | ||||||
rrl | 1476695 | n.3038T>A | non_coding_transcript_exon_variant | 0.22 | capreomycin | |
linezolid | ||||||
rrl | 1476723 | n.3066T>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
linezolid | ||||||
rrl | 1476726 | n.3069A>G | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
linezolid | ||||||
fabG1 | 1673338 | c.-102G>A | upstream_gene_variant | 1.0 | ethionamide | |
isoniazid | ||||||
rpsA | 1834609 | c.1068T>C | synonymous_variant | 0.14 | pyrazinamide | |
rpsA | 1834633 | c.1092A>G | synonymous_variant | 0.15 | pyrazinamide | |
rpsA | 1834639 | c.1098T>C | synonymous_variant | 0.15 | pyrazinamide | |
rpsA | 1834654 | p.Glu371Asp | missense_variant | 0.15 | pyrazinamide | |
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 | streptomycin | Not assoc w R |
kanamycin | Not assoc w R | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
ndh | 2101921 | c.1122G>A | synonymous_variant | 0.97 | ethionamide | Not assoc w R - Interim |
delamanid | Not assoc w R - Interim | |||||
isoniazid | Not assoc w R - Interim | |||||
ndh | 2103112 | c.-70G>T | upstream_gene_variant | 1.0 | ethionamide | Uncertain significance |
delamanid | Uncertain significance | |||||
isoniazid | Not assoc w R - Interim | |||||
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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
pncA | 2290062 | c.-821G>A | upstream_gene_variant | 0.97 | pyrazinamide | |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
Rv2477c | 2783116 | c.927T>C | synonymous_variant | 0.13 | ethambutol | |
moxifloxacin | ||||||
streptomycin | ||||||
levofloxacin | ||||||
kanamycin | ||||||
rifampicin | ||||||
amikacin | ||||||
Rv2477c | 2783914 | c.129T>C | synonymous_variant | 0.13 | ethambutol | |
moxifloxacin | ||||||
streptomycin | ||||||
levofloxacin | ||||||
kanamycin | ||||||
rifampicin | ||||||
amikacin | ||||||
Rv2477c | 2783920 | c.123G>C | synonymous_variant | 0.14 | ethambutol | |
moxifloxacin | ||||||
streptomycin | ||||||
levofloxacin | ||||||
kanamycin | ||||||
rifampicin | ||||||
amikacin | ||||||
Rv2752c | 3064664 | p.Lys510Gln | missense_variant | 0.98 | ethambutol | Uncertain significance |
moxifloxacin | ||||||
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
thyX | 3067949 | c.-4C>T | upstream_gene_variant | 0.99 | para-aminosalicylic_acid | |
thyA | 3073920 | c.552C>G | synonymous_variant | 0.14 | para-aminosalicylic_acid | |
thyA | 3073977 | c.495A>G | synonymous_variant | 0.14 | para-aminosalicylic_acid | |
ald | 3087084 | c.266delA | frameshift_variant | 1.0 | cycloserine | |
ald | 3087172 | p.Glu118Ala | missense_variant | 0.99 | cycloserine | |
ald | 3087184 | c.368_373delCCGACG | disruptive_inframe_deletion | 1.0 | cycloserine | |
Rv3236c | 3612237 | p.Ala294Ser | missense_variant | 0.99 | pyrazinamide | |
lpqB | 3624350 | c.561G>T | synonymous_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
rifampicin | Not assoc w R | |||||
lpqB | 3624486 | p.Asp142Gly | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
alr | 3840932 | c.489C>T | synonymous_variant | 0.98 | cycloserine | |
rpoA | 3877679 | p.Ala277Ser | missense_variant | 0.14 | rifampicin | |
rpoA | 3877692 | c.816G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoA | 3877743 | c.765T>C | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoA | 3877764 | c.744C>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoA | 3877770 | c.738A>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoA | 3877782 | c.726T>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoA | 3877791 | c.717C>G | synonymous_variant | 0.14 | rifampicin | |
ddn | 3986987 | c.144G>T | synonymous_variant | 1.0 | delamanid | Not assoc w R - Interim |
pretomanid | ||||||
ddn | 3987180 | p.Asp113Asn | missense_variant | 1.0 | delamanid | Uncertain significance |
pretomanid | ||||||
clpC1 | 4038755 | c.1950G>C | synonymous_variant | 0.14 | pyrazinamide | |
clpC1 | 4040824 | c.-120C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
glpK | 4138377 | p.Val460Ala | missense_variant | 1.0 | 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 | 4139131 | p.Glu209Lys | missense_variant | 1.0 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
rifampicin | Not assoc w R | |||||
isoniazid | 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 | 0.98 | ethambutol | Not assoc w R - Interim |
embA | 4245147 | p.Pro639Ser | missense_variant | 0.92 | ethambutol | Not assoc w R - Interim |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4249495 | c.2982C>T | synonymous_variant | 0.94 | 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 | 4326914 | p.Ala187Glu | missense_variant | 1.0 | ethionamide | Uncertain significance |
ethA | 4327103 | p.Gly124Asp | missense_variant | 1.0 | ethionamide | Uncertain significance |
ethR | 4328190 | p.Glu214Asp | missense_variant | 1.0 | ethionamide | |
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 | 1.0 | streptomycin | Not assoc w R |
gid | 4407946 | p.Leu86Pro | missense_variant | 1.0 | streptomycin | Uncertain significance |