Run ID: ERR4821318
Sample name:
Date: 2024-10-04T17:51:18.175225
Number of reads: 3408955
Percentage reads mapped: 93.86
Median coverage: 78.0
Strain: lineage4.6.2.2
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.6 | Euro-American | None | 1.0 |
lineage4.6.2 | Euro-American | RD726 | 1.0 |
lineage4.6.2.2 | Euro-American (Cameroon) | RD726 | 1.0 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ethambutol | ||||
pyrazinamide | ||||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | rrs | n.1402C>A | Uncertain significance | Mutation from literature |
capreomycin | rrs | n.1402C>A | Uncertain significance | Mutation from literature |
kanamycin | rrs | n.1402C>A | Uncertain significance | Mutation from literature |
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rrs | 1473247 | n.1402C>A | non_coding_transcript_exon_variant | 0.44 | amikacin | Uncertain significance | Mutation from literature |
capreomycin | Uncertain significance | Mutation from literature | |||||
kanamycin | Uncertain significance | Mutation from literature | |||||
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 1.0 | ethionamide | Assoc w R | Alias fabG1_c.-15C>T |
isoniazid | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
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 | |||||
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 778298 | c.183G>A | synonymous_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472148 | n.303T>C | non_coding_transcript_exon_variant | 0.56 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.56 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472160 | n.315C>T | non_coding_transcript_exon_variant | 0.62 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472188 | n.343A>G | non_coding_transcript_exon_variant | 0.76 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472225 | n.380C>G | non_coding_transcript_exon_variant | 0.79 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472240 | n.395G>A | non_coding_transcript_exon_variant | 0.73 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472251 | n.406G>C | non_coding_transcript_exon_variant | 0.85 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.6 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472623 | n.778A>C | non_coding_transcript_exon_variant | 0.57 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472647 | n.802C>T | non_coding_transcript_exon_variant | 0.72 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472674 | n.829T>C | non_coding_transcript_exon_variant | 0.82 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472675 | n.830T>G | non_coding_transcript_exon_variant | 0.82 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472677 | n.832C>A | non_coding_transcript_exon_variant | 0.82 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472682 | n.837T>A | non_coding_transcript_exon_variant | 0.82 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472683 | n.838T>C | non_coding_transcript_exon_variant | 0.82 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472685 | n.840G>T | non_coding_transcript_exon_variant | 0.82 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472701 | n.856T>C | non_coding_transcript_exon_variant | 0.87 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472767 | n.922G>C | non_coding_transcript_exon_variant | 0.75 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472790 | n.945T>C | non_coding_transcript_exon_variant | 0.74 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472952 | n.1107T>C | non_coding_transcript_exon_variant | 0.67 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.57 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472957 | n.1112C>A | non_coding_transcript_exon_variant | 0.57 | kanamycin | |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472969 | n.1125delC | non_coding_transcript_exon_variant | 0.57 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472973 | n.1128A>T | non_coding_transcript_exon_variant | 0.57 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472974 | n.1129A>C | non_coding_transcript_exon_variant | 0.57 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472975 | n.1130T>G | non_coding_transcript_exon_variant | 0.57 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472977 | n.1132G>C | non_coding_transcript_exon_variant | 0.6 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472989 | n.1144G>T | non_coding_transcript_exon_variant | 0.65 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.65 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472996 | n.1151T>C | non_coding_transcript_exon_variant | 0.81 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473029 | n.1184C>G | non_coding_transcript_exon_variant | 0.67 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.37 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473226 | n.1381C>G | non_coding_transcript_exon_variant | 0.48 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473276 | n.1431A>G | non_coding_transcript_exon_variant | 0.31 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473284 | n.1439A>G | non_coding_transcript_exon_variant | 0.23 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473285 | n.1440A>T | non_coding_transcript_exon_variant | 0.23 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473290 | n.1445C>T | non_coding_transcript_exon_variant | 0.2 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1473292 | n.1447_1449delGGAinsTGGG | non_coding_transcript_exon_variant | 0.21 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473301 | n.1456T>C | non_coding_transcript_exon_variant | 0.24 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1475916 | n.2259C>T | non_coding_transcript_exon_variant | 0.46 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475943 | n.2286G>A | non_coding_transcript_exon_variant | 0.6 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475952 | n.2295A>G | non_coding_transcript_exon_variant | 0.61 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475977 | n.2320A>G | non_coding_transcript_exon_variant | 0.71 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475978 | n.2321C>T | non_coding_transcript_exon_variant | 0.71 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 0.67 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1475991 | n.2334T>A | non_coding_transcript_exon_variant | 0.67 | capreomycin | |
linezolid | ||||||
rrl | 1475997 | n.2340A>G | non_coding_transcript_exon_variant | 0.71 | capreomycin | |
linezolid | ||||||
rrl | 1476001 | n.2344T>C | non_coding_transcript_exon_variant | 0.67 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476187 | n.2530T>C | non_coding_transcript_exon_variant | 0.78 | capreomycin | |
linezolid | ||||||
rrl | 1476194 | n.2537A>G | non_coding_transcript_exon_variant | 0.81 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476200 | n.2543A>T | non_coding_transcript_exon_variant | 0.85 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476207 | n.2550T>C | non_coding_transcript_exon_variant | 0.85 | capreomycin | |
linezolid | ||||||
rrl | 1476214 | n.2557G>T | non_coding_transcript_exon_variant | 0.83 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476221 | n.2564T>C | non_coding_transcript_exon_variant | 0.8 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 0.77 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476235 | n.2578A>G | non_coding_transcript_exon_variant | 0.62 | capreomycin | |
linezolid | ||||||
rrl | 1476245 | n.2588C>T | non_coding_transcript_exon_variant | 0.67 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.92 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476363 | n.2706A>G | non_coding_transcript_exon_variant | 0.92 | capreomycin | |
linezolid | ||||||
rrl | 1476366 | n.2709A>C | non_coding_transcript_exon_variant | 0.85 | capreomycin | |
linezolid | ||||||
rrl | 1476368 | n.2711T>C | non_coding_transcript_exon_variant | 0.79 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.79 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.79 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476374 | n.2717T>G | non_coding_transcript_exon_variant | 0.79 | capreomycin | |
linezolid | ||||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.82 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.67 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.67 | capreomycin | Uncertain significance |
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 | 2063187 | c.1542C>T | synonymous_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R - Interim | |||||
streptomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
katG | 2155389 | c.723C>G | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
Rv1979c | 2221746 | c.1416_1418dupCCG | disruptive_inframe_insertion | 0.98 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv2680 | 2996208 | p.Ala35Asp | missense_variant | 1.0 | capreomycin | Uncertain significance |
thyX | 3067474 | p.Pro158Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
Rv3083 | 3448567 | p.His22Asp | missense_variant | 1.0 | ethionamide | Uncertain significance |
Rv3236c | 3612571 | c.546C>T | synonymous_variant | 0.99 | pyrazinamide | Not assoc w R |
Rv3236c | 3612910 | p.Leu69Phe | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
embC | 4242550 | c.2688C>G | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4245700 | p.Gly823Glu | missense_variant | 1.0 | ethambutol | Uncertain significance |
aftB | 4267272 | p.Lys522Arg | missense_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4326739 | c.735C>G | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
ethR | 4328004 | c.456G>A | synonymous_variant | 1.0 | ethionamide | 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 |