Run ID: ERR2514279
Sample name:
Date: 2024-10-05T07:08:02.680261
Number of reads: 3153754
Percentage reads mapped: 97.28
Median coverage: 97.0
Strain: lineage3
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 1.0 |
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 | 94 | p.Ser32Gly | missense_variant | 1.0 | isoniazid | 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.99 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
mshA | 576759 | p.His471Pro | missense_variant | 1.0 | isoniazid | Uncertain significance |
ethionamide | ||||||
Rv0565c | 656882 | p.Pro197Ala | missense_variant | 1.0 | ethionamide | |
Rv0565c | 657081 | c.390G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
nusG | 734202 | c.-52G>C | upstream_gene_variant | 1.0 | rifampicin | Uncertain significance |
mmaA3 | 738010 | p.Asp47Gly | missense_variant | 0.99 | isoniazid | |
rpoB | 762434 | c.2628T>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
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 | 1254039 | p.Asn166Asp | missense_variant | 0.98 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
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 | |||||
rrs | 1471601 | n.-245A>G | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472122 | n.277G>T | non_coding_transcript_exon_variant | 0.17 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472123 | n.278A>T | non_coding_transcript_exon_variant | 0.17 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472124 | n.279C>T | non_coding_transcript_exon_variant | 0.17 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.34 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472155 | n.310C>T | non_coding_transcript_exon_variant | 0.24 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472160 | n.315C>T | non_coding_transcript_exon_variant | 0.24 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472251 | n.406G>A | non_coding_transcript_exon_variant | 0.2 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.28 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.28 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472895 | n.1050C>T | non_coding_transcript_exon_variant | 0.33 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472954 | n.1109T>C | non_coding_transcript_exon_variant | 0.24 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.42 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.42 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472973 | n.1128A>G | non_coding_transcript_exon_variant | 0.31 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472987 | n.1142G>A | non_coding_transcript_exon_variant | 0.22 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.22 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.41 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472992 | n.1147A>G | non_coding_transcript_exon_variant | 0.15 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473005 | n.1160C>T | non_coding_transcript_exon_variant | 0.18 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.51 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.44 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.45 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473066 | n.1221A>G | non_coding_transcript_exon_variant | 0.47 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473088 | n.1243A>G | non_coding_transcript_exon_variant | 0.39 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473093 | n.1248C>T | non_coding_transcript_exon_variant | 0.38 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473100 | n.1255G>A | non_coding_transcript_exon_variant | 0.37 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473102 | n.1257C>T | non_coding_transcript_exon_variant | 0.35 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473104 | n.1259C>T | non_coding_transcript_exon_variant | 0.37 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473110 | n.1265T>G | non_coding_transcript_exon_variant | 0.37 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473111 | n.1266A>G | non_coding_transcript_exon_variant | 0.37 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473115 | n.1270G>T | non_coding_transcript_exon_variant | 0.24 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473121 | n.1276T>C | non_coding_transcript_exon_variant | 0.4 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473123 | n.1278A>T | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.44 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.33 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473172 | n.1327T>G | non_coding_transcript_exon_variant | 0.18 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473173 | n.1328C>T | non_coding_transcript_exon_variant | 0.18 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1473221 | n.1376C>T | non_coding_transcript_exon_variant | 0.21 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473252 | n.1407T>C | non_coding_transcript_exon_variant | 0.31 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473259 | n.1414C>T | non_coding_transcript_exon_variant | 0.3 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473276 | n.1431A>C | non_coding_transcript_exon_variant | 0.22 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473277 | n.1432G>A | non_coding_transcript_exon_variant | 0.19 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1473300 | n.1455C>T | non_coding_transcript_exon_variant | 0.14 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473301 | n.1456T>G | non_coding_transcript_exon_variant | 0.18 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473316 | n.1471C>T | non_coding_transcript_exon_variant | 0.26 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1475898 | n.2241A>G | non_coding_transcript_exon_variant | 0.35 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.25 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.37 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.33 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>T | non_coding_transcript_exon_variant | 0.27 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.39 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.31 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.27 | capreomycin | Not assoc w R |
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 |
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 | 2167998 | p.Pro872Gln | missense_variant | 0.99 | 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 | 2289365 | c.-125delC | upstream_gene_variant | 0.99 | pyrazinamide | |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 | isoniazid | Not assoc w R |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 1.0 | kanamycin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
clpC1 | 4040264 | c.441C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
embC | 4241542 | c.1680C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
aftB | 4268003 | c.834G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
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 |