Run ID: ERR4816009
Sample name:
Date: 2024-03-24T19:00:29.192851
Number of reads: 594769
Percentage reads mapped: 90.62
Median coverage: 19.0
Strain: lineage1.1.2
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage1.1.2 | Indo-Oceanic | RD239 | 1.0 |
lineage1.1 | Indo-Oceanic | RD239 | 1.0 |
lineage1 | Indo-Oceanic | RD239 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | rrs | n.799C>T | 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 | 1472644 | n.799C>T | non_coding_transcript_exon_variant | 0.48 | streptomycin | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrB | 6124 | c.885C>T | synonymous_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 | 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 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
Rv0565c | 656756 | p.His239Tyr | missense_variant | 1.0 | ethionamide | |
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 1.0 | ethionamide | |
hadA | 732154 | c.225G>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
nusG | 734116 | c.-138T>C | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
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 | 800250 | c.-559C>G | upstream_gene_variant | 1.0 | linezolid | |
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 | |||||
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 | ||||||
rrs | 1471668 | n.-178G>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.69 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.68 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472251 | n.406G>A | non_coding_transcript_exon_variant | 0.61 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.59 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472597 | n.752G>A | non_coding_transcript_exon_variant | 0.42 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472607 | n.762G>A | non_coding_transcript_exon_variant | 0.48 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472655 | n.810G>T | non_coding_transcript_exon_variant | 0.67 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472660 | n.815T>C | non_coding_transcript_exon_variant | 0.58 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472714 | n.869A>G | non_coding_transcript_exon_variant | 0.56 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472952 | n.1107T>C | non_coding_transcript_exon_variant | 0.48 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472955 | n.1110C>T | non_coding_transcript_exon_variant | 0.52 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.58 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.56 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472973 | n.1128A>T | non_coding_transcript_exon_variant | 0.59 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472987 | n.1142G>A | non_coding_transcript_exon_variant | 0.55 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.52 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.64 | streptomycin | Uncertain significance |
kanamycin | Not assoc w R | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.79 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.87 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.86 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473066 | n.1221A>G | non_coding_transcript_exon_variant | 0.84 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473088 | n.1243A>G | non_coding_transcript_exon_variant | 0.71 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473093 | n.1248C>T | non_coding_transcript_exon_variant | 0.67 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473100 | n.1255G>A | non_coding_transcript_exon_variant | 0.63 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473102 | n.1257C>T | non_coding_transcript_exon_variant | 0.5 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473104 | n.1259C>T | non_coding_transcript_exon_variant | 0.63 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473110 | n.1265T>G | non_coding_transcript_exon_variant | 0.65 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473111 | n.1266A>G | non_coding_transcript_exon_variant | 0.62 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473115 | n.1270G>T | non_coding_transcript_exon_variant | 0.34 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473121 | n.1276T>C | non_coding_transcript_exon_variant | 0.66 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.56 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.54 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473259 | n.1414C>T | non_coding_transcript_exon_variant | 0.5 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473316 | n.1471C>T | non_coding_transcript_exon_variant | 0.44 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.48 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.56 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.53 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.42 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.52 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.55 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
tsnR | 1853974 | c.369C>T | synonymous_variant | 1.0 | linezolid | Not assoc w R |
tsnR | 1854045 | p.Tyr147Cys | missense_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 |
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 | |||||
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 | isoniazid | |
Rv2681 | 2996912 | c.174C>T | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
fbiD | 3339741 | c.624G>A | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 | ethionamide | Uncertain significance |
lpqB | 3623901 | p.Pro337His | missense_variant | 1.0 | bedaquiline | |
rifampicin | 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 | |||||
fbiA | 3641357 | p.Val272Ala | missense_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 | 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 | 1.0 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243848 | p.Val206Met | missense_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 | 4328209 | c.-736C>A | upstream_gene_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 | 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 |
gid | 4407935 | p.Leu90Val | missense_variant | 1.0 | streptomycin | Uncertain significance |
gid | 4407944 | p.Gln87Glu | missense_variant | 1.0 | streptomycin | Uncertain significance |