Run ID: SRR13861235
Sample name:
Date: 2024-04-15T07:52:45.732146
Number of reads: 2629915
Percentage reads mapped: 43.88
Median coverage: 90.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.9 | Euro-American (H37Rv-like) | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | katG | p.Gly234Glu | Uncertain significance | Mutation from literature |
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 |
---|---|---|---|---|---|---|---|
katG | 2155411 | p.Gly234Glu | missense_variant | 1.0 | isoniazid | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 7760 | c.459C>T | synonymous_variant | 0.12 | levofloxacin | |
moxifloxacin | ||||||
Rv0010c | 13524 | p.Gly12Ala | missense_variant | 1.0 | isoniazid | |
mshA | 576259 | c.912C>T | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
isoniazid | Not assoc w R - Interim | |||||
ccsA | 620690 | p.Val267Glu | missense_variant | 0.89 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
Rv0565c | 657622 | c.-152G>A | upstream_gene_variant | 0.94 | ethionamide | |
rpoB | 759805 | c.-2T>C | upstream_gene_variant | 1.0 | rifampicin | |
rpoB | 761961 | p.Pro719Thr | missense_variant | 0.88 | rifampicin | |
rpoC | 763528 | c.159G>A | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 764895 | p.Ile509Thr | missense_variant | 0.92 | rifampicin | |
rpoC | 766672 | c.3303T>C | synonymous_variant | 0.14 | rifampicin | |
rpoC | 766726 | c.3357T>C | synonymous_variant | 0.14 | rifampicin | |
rpoC | 766738 | c.3369G>T | 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 | 0.15 | rifampicin | |
rpoC | 766801 | c.3432C>A | synonymous_variant | 0.13 | rifampicin | |
rpoC | 766804 | c.3435A>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
mmpL5 | 777574 | p.Phe303Leu | missense_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
mmpL5 | 777578 | c.903C>G | synonymous_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
mmpL5 | 778982 | c.-502A>C | upstream_gene_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
rplC | 801169 | p.Lys121* | stop_gained | 0.93 | linezolid | |
rrs | 1472061 | n.216A>T | non_coding_transcript_exon_variant | 0.13 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.14 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1474052 | n.395G>T | non_coding_transcript_exon_variant | 0.95 | capreomycin | |
linezolid | ||||||
rrl | 1474794 | n.1137C>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474904 | n.1247G>A | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
linezolid | ||||||
rrl | 1475419 | n.1762C>T | non_coding_transcript_exon_variant | 0.21 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475483 | n.1826C>T | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475505 | n.1848G>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475599 | n.1942A>G | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
linezolid | Uncertain significance | |||||
rrl | 1475608 | n.1951T>C | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475638 | n.1981C>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
linezolid | ||||||
rrl | 1475642 | n.1985T>C | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
linezolid | ||||||
rrl | 1475657 | n.2000A>G | non_coding_transcript_exon_variant | 0.17 | capreomycin | |
linezolid | ||||||
rrl | 1475659 | n.2002G>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
linezolid | ||||||
rrl | 1475763 | n.2106C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
linezolid | ||||||
rrl | 1476479 | n.2822T>G | non_coding_transcript_exon_variant | 0.88 | capreomycin | |
linezolid | ||||||
rrl | 1476583 | n.2926G>A | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
linezolid | ||||||
rpsA | 1834375 | c.834G>A | synonymous_variant | 0.13 | pyrazinamide | |
rpsA | 1834417 | c.876G>C | synonymous_variant | 0.15 | pyrazinamide | |
rpsA | 1834423 | c.882G>C | synonymous_variant | 0.15 | pyrazinamide | |
rpsA | 1834435 | c.894G>C | synonymous_variant | 0.15 | pyrazinamide | |
tlyA | 1918432 | p.Pro165Thr | missense_variant | 1.0 | capreomycin | |
ndh | 2101769 | p.Arg425His | missense_variant | 1.0 | ethionamide | |
delamanid | ||||||
isoniazid | Uncertain significance | |||||
katG | 2155508 | p.Ala202Ser | missense_variant | 1.0 | isoniazid | Uncertain significance |
pncA | 2289474 | c.-233C>G | upstream_gene_variant | 1.0 | pyrazinamide | |
kasA | 2518519 | c.405G>C | synonymous_variant | 0.13 | isoniazid | |
kasA | 2518540 | c.426T>G | synonymous_variant | 0.14 | isoniazid | |
folC | 2746862 | p.Leu246Arg | missense_variant | 1.0 | para-aminosalicylic_acid | |
folC | 2747268 | p.Asp111His | missense_variant | 0.96 | para-aminosalicylic_acid | |
Rv2752c | 3065109 | c.1083A>G | synonymous_variant | 0.99 | ethambutol | |
moxifloxacin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
Rv2752c | 3066839 | c.-648A>G | upstream_gene_variant | 0.13 | ethambutol | |
moxifloxacin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
whiB7 | 3568816 | c.-137C>T | upstream_gene_variant | 1.0 | streptomycin | |
amikacin | ||||||
kanamycin | ||||||
whiB7 | 3569222 | c.-543G>A | upstream_gene_variant | 0.99 | streptomycin | |
amikacin | ||||||
kanamycin | ||||||
lpqB | 3624508 | p.Ile135Val | missense_variant | 0.97 | bedaquiline | |
rifampicin | ||||||
mtrB | 3625247 | p.Arg456Pro | missense_variant | 0.97 | bedaquiline | |
rifampicin | ||||||
rpoA | 3878049 | c.459G>C | synonymous_variant | 0.14 | rifampicin | |
rpoA | 3878055 | c.453A>G | synonymous_variant | 0.15 | rifampicin | |
rpoA | 3878061 | c.447G>C | synonymous_variant | 0.16 | rifampicin | |
rpoA | 3878067 | c.441C>G | synonymous_variant | 0.14 | rifampicin | |
rpoA | 3878070 | c.438T>C | synonymous_variant | 0.15 | rifampicin | |
rpoA | 3878082 | c.426T>C | synonymous_variant | 0.14 | rifampicin | |
clpC1 | 4038468 | p.Asp746Gly | missense_variant | 0.89 | pyrazinamide | |
clpC1 | 4038536 | c.2169C>T | synonymous_variant | 0.13 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4039085 | c.1620A>G | synonymous_variant | 0.14 | pyrazinamide | |
clpC1 | 4039090 | c.1615C>T | synonymous_variant | 0.14 | pyrazinamide | |
clpC1 | 4039097 | c.1608G>C | synonymous_variant | 0.14 | pyrazinamide | |
clpC1 | 4039103 | c.1602T>C | synonymous_variant | 0.13 | pyrazinamide | |
clpC1 | 4039106 | c.1599G>C | synonymous_variant | 0.14 | pyrazinamide | |
clpC1 | 4039112 | c.1593C>G | synonymous_variant | 0.14 | pyrazinamide | |
clpC1 | 4039142 | c.1563A>G | synonymous_variant | 0.14 | pyrazinamide | |
clpC1 | 4039145 | c.1560G>C | synonymous_variant | 0.14 | pyrazinamide | |
clpC1 | 4039169 | p.Glu512Asp | missense_variant | 0.14 | pyrazinamide | |
clpC1 | 4039172 | c.1533A>G | synonymous_variant | 0.15 | pyrazinamide | |
clpC1 | 4039178 | c.1527G>C | synonymous_variant | 0.14 | pyrazinamide | |
clpC1 | 4039183 | c.1522T>C | synonymous_variant | 0.14 | pyrazinamide | |
clpC1 | 4040148 | p.Lys186Ile | missense_variant | 0.96 | pyrazinamide | |
embC | 4240125 | p.Cys88Tyr | missense_variant | 0.95 | ethambutol | |
embC | 4240726 | c.864G>C | synonymous_variant | 0.13 | ethambutol | Not assoc w R - Interim |
embC | 4240780 | c.918T>C | synonymous_variant | 0.15 | ethambutol | |
embC | 4240783 | c.921G>C | synonymous_variant | 0.16 | ethambutol | |
embC | 4240789 | c.927T>C | synonymous_variant | 0.16 | ethambutol | |
embB | 4248085 | c.1572T>C | synonymous_variant | 0.15 | ethambutol | |
embB | 4248097 | c.1584C>G | synonymous_variant | 0.16 | ethambutol | |
embB | 4248118 | c.1605T>C | synonymous_variant | 0.13 | ethambutol | |
embB | 4248157 | c.1644A>G | synonymous_variant | 0.14 | ethambutol | Not assoc w R - Interim |
embB | 4248208 | p.Ser565Arg | missense_variant | 0.15 | ethambutol | |
embB | 4248220 | c.1707A>G | synonymous_variant | 0.17 | ethambutol | Not assoc w R - Interim |
embB | 4248241 | c.1728C>T | synonymous_variant | 0.19 | ethambutol | |
embB | 4248265 | c.1752C>T | synonymous_variant | 0.16 | ethambutol | |
embB | 4248266 | c.1753C>T | synonymous_variant | 0.17 | ethambutol | |
embB | 4248277 | c.1764G>C | synonymous_variant | 0.15 | ethambutol | |
ethR | 4327643 | p.Thr32Ile | missense_variant | 0.99 | ethionamide |