Run ID: ERR4796584
Sample name:
Date: 2024-03-26T16:00:57.135037
Number of reads: 2525885
Percentage reads mapped: 93.44
Median coverage: 70.0
Strain: lineage1.2.2.2
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage1.2.2 | Indo-Oceanic | RD239 | 1.0 |
lineage1.2.2.2 | Indo-Oceanic | RD239 | 1.0 |
lineage1 | Indo-Oceanic | RD239 | 0.98 |
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 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1353 | c.1353T>C | synonymous_variant | 0.13 | isoniazid | |
dnaA | 1375 | c.1375T>C | synonymous_variant | 0.16 | isoniazid | |
dnaA | 1383 | c.1383A>G | synonymous_variant | 0.15 | isoniazid | |
dnaA | 1389 | c.1389C>G | synonymous_variant | 0.15 | isoniazid | |
dnaA | 1392 | c.1392A>G | synonymous_variant | 0.15 | isoniazid | |
dnaA | 1395 | c.1395G>C | synonymous_variant | 0.14 | isoniazid | |
dnaA | 1404 | c.1404T>C | synonymous_variant | 0.15 | isoniazid | |
dnaA | 1407 | c.1407T>C | synonymous_variant | 0.13 | isoniazid | |
dnaA | 1413 | c.1413A>C | synonymous_variant | 0.14 | isoniazid | |
dnaA | 1416 | c.1416C>G | synonymous_variant | 0.14 | isoniazid | |
dnaA | 1428 | c.1428C>G | synonymous_variant | 0.12 | isoniazid | |
dnaA | 1431 | c.1431A>G | synonymous_variant | 0.13 | isoniazid | |
dnaA | 1449 | c.1449G>A | synonymous_variant | 0.12 | isoniazid | |
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7268 | c.-34C>T | upstream_gene_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
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 | 7943 | p.Glu214Asp | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
gyrA | 8452 | p.Ala384Val | 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 | |||||
Rv0010c | 13298 | p.Ile87Met | missense_variant | 1.0 | isoniazid | Not assoc w R |
Rv0010c | 13460 | c.99T>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
Rv0010c | 13548 | p.Thr4Ile | missense_variant | 1.0 | isoniazid | Not assoc w R |
Rv0010c | 13699 | c.-141A>G | upstream_gene_variant | 1.0 | isoniazid | Not assoc w R |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 1.0 | ethionamide | |
nusG | 734116 | c.-138T>C | upstream_gene_variant | 0.98 | rifampicin | Not assoc w R |
rpoC | 762989 | c.-381G>C | upstream_gene_variant | 0.15 | rifampicin | |
rpoC | 763013 | c.-357C>G | upstream_gene_variant | 0.2 | rifampicin | |
rpoB | 763028 | c.3222T>C | synonymous_variant | 0.23 | rifampicin | Not assoc w R - Interim |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.77 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>G | synonymous_variant | 0.23 | rifampicin | Not assoc w R - Interim |
rpoB | 763034 | c.3228C>G | synonymous_variant | 0.23 | rifampicin | Not assoc w R - Interim |
rpoB | 763040 | c.3234C>G | synonymous_variant | 0.23 | rifampicin | Not assoc w R - Interim |
rpoB | 763070 | c.3264T>C | synonymous_variant | 0.25 | rifampicin | Not assoc w R - Interim |
rpoB | 763085 | c.3279C>G | synonymous_variant | 0.23 | rifampicin | Not assoc w R - Interim |
rpoB | 763115 | c.3309T>C | synonymous_variant | 0.2 | rifampicin | Not assoc w R - Interim |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.93 | rifampicin | Not assoc w R |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.92 | rifampicin | Not assoc w R |
rpoC | 766726 | c.3357T>C | synonymous_variant | 0.15 | rifampicin | |
rpoC | 766738 | c.3369G>C | synonymous_variant | 0.16 | rifampicin | |
rpoC | 766765 | c.3396A>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 766774 | c.3405T>C | synonymous_variant | 0.14 | rifampicin | |
rpoC | 766801 | c.3432C>G | synonymous_variant | 0.13 | rifampicin | |
rpoC | 767059 | c.3690T>G | synonymous_variant | 0.12 | 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 |
rplC | 800357 | c.-452C>A | upstream_gene_variant | 1.0 | linezolid | Not assoc w R |
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 | |||||
Rv1129c | 1254747 | c.-213C>A | upstream_gene_variant | 1.0 | moxifloxacin | |
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
fbiC | 1303884 | c.954T>G | synonymous_variant | 0.12 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 | ethambutol | Not assoc w R |
embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | |
embR | 1417793 | c.-446C>T | upstream_gene_variant | 1.0 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1473877 | n.220G>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
linezolid | ||||||
rrl | 1473898 | n.241C>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1473943 | n.286G>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1473945 | n.288T>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1473946 | n.289A>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1473986 | n.329T>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
linezolid | ||||||
rpsA | 1834633 | c.1092A>G | synonymous_variant | 0.17 | pyrazinamide | |
rpsA | 1834639 | c.1098T>C | synonymous_variant | 0.13 | pyrazinamide | |
rpsA | 1834654 | p.Glu371Asp | missense_variant | 0.13 | pyrazinamide | |
rpsA | 1834684 | c.1143C>T | synonymous_variant | 0.14 | pyrazinamide | |
tsnR | 1853974 | c.369C>T | synonymous_variant | 1.0 | linezolid | 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 | 1.0 | streptomycin | Not assoc w R |
kanamycin | Not assoc w R | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
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 | 2168742 | p.Gly624Asp | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | 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 | |||||
Rv1979c | 2223553 | c.-389C>A | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Uncertain significance | |||||
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 | isoniazid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 | ethionamide | Uncertain significance |
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 | |||||
mtrB | 3626467 | c.147G>A | synonymous_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
rifampicin | Not assoc w R | |||||
rpoA | 3878817 | c.-310T>A | upstream_gene_variant | 0.81 | rifampicin | Not assoc w R |
rpoA | 3878878 | c.-371T>C | upstream_gene_variant | 0.14 | rifampicin | Uncertain significance |
rpoA | 3878890 | c.-383C>G | upstream_gene_variant | 0.2 | rifampicin | |
rpoA | 3878909 | c.-402A>G | upstream_gene_variant | 0.16 | rifampicin | |
rpoA | 3878914 | c.-407T>C | upstream_gene_variant | 0.16 | rifampicin | Uncertain significance |
clpC1 | 4038425 | c.2280C>T | synonymous_variant | 0.97 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.92 | pyrazinamide | Not assoc w R - Interim |
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 | |||||
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.98 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
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 | 4326148 | c.1326G>T | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
ethA | 4326439 | p.Asn345Lys | missense_variant | 1.0 | ethionamide | Uncertain significance |
whiB6 | 4338203 | p.Arg107Cys | missense_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | 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 | 4338603 | c.-82C>T | 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 | 4407873 | c.330G>T | synonymous_variant | 1.0 | streptomycin | Not assoc w R |