Run ID: SRR3675448
Sample name:
Date: 2024-10-05T02:25:20.185866
Number of reads: 80885
Percentage reads mapped: 18.54
Median coverage: 2.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 0.99 |
lineage4.9 | Euro-American (H37Rv-like) | None | 0.99 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | rrs | n.462C>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 | 1472307 | n.462C>T | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
rpoB | 763070 | c.3264T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoB | 763085 | c.3279C>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoB | 763115 | c.3309T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoB | 763136 | c.3330C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 763546 | c.177A>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 763570 | c.201G>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 763573 | c.204G>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 763603 | c.234C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 766861 | c.3492G>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 766864 | c.3495G>C | synonymous_variant | 1.0 | rifampicin | |
rpoC | 766867 | c.3498C>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 766885 | c.3516G>A | synonymous_variant | 1.0 | rifampicin | |
rpoC | 766894 | c.3525T>C | synonymous_variant | 1.0 | rifampicin | |
rpoC | 766900 | c.3531T>C | synonymous_variant | 1.0 | rifampicin | |
rpoC | 767119 | c.3750A>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 767134 | c.3765C>A | synonymous_variant | 1.0 | rifampicin | |
rpoC | 767158 | c.3789T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 767180 | p.Ala1271Gln | missense_variant | 1.0 | rifampicin | |
rpoC | 767191 | c.3822C>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpsL | 781700 | c.141G>C | synonymous_variant | 1.0 | streptomycin | |
rpsL | 781703 | c.144G>T | synonymous_variant | 1.0 | streptomycin | |
rpsL | 781715 | c.156T>C | synonymous_variant | 1.0 | streptomycin | |
rpsL | 781728 | c.169T>C | synonymous_variant | 1.0 | streptomycin | |
rpsL | 781736 | c.177T>C | synonymous_variant | 1.0 | streptomycin | |
rpsL | 781742 | c.183C>T | synonymous_variant | 1.0 | streptomycin | |
rpsL | 781748 | c.189C>G | synonymous_variant | 1.0 | streptomycin | |
rpsL | 781754 | c.195G>C | synonymous_variant | 1.0 | streptomycin | |
rpsL | 781760 | c.201T>C | synonymous_variant | 1.0 | streptomycin | |
rpsL | 781772 | c.213C>A | synonymous_variant | 1.0 | streptomycin | |
rrs | 1472061 | n.216A>T | non_coding_transcript_exon_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472075 | n.230A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472108 | n.263C>T | non_coding_transcript_exon_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472300 | n.455C>T | non_coding_transcript_exon_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472969 | n.1124A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472970 | n.1125C>G | non_coding_transcript_exon_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472977 | n.1132G>C | non_coding_transcript_exon_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472978 | n.1133T>C | non_coding_transcript_exon_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473105 | n.1260G>A | non_coding_transcript_exon_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1473123 | n.1278delAinsTT | non_coding_transcript_exon_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473290 | n.1445C>T | non_coding_transcript_exon_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrl | 1473417 | n.-241C>T | upstream_gene_variant | 0.9 | capreomycin | |
linezolid | ||||||
rrl | 1473419 | n.-239T>C | upstream_gene_variant | 0.9 | capreomycin | |
linezolid | ||||||
rrl | 1473420 | n.-238A>G | upstream_gene_variant | 0.9 | capreomycin | |
linezolid | ||||||
rrl | 1473421 | n.-237G>A | upstream_gene_variant | 0.9 | capreomycin | |
linezolid | ||||||
rrl | 1473756 | n.99G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1473758 | n.101G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1473806 | n.149C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1473877 | n.220G>A | non_coding_transcript_exon_variant | 0.95 | capreomycin | |
linezolid | ||||||
rrl | 1473898 | n.241C>T | non_coding_transcript_exon_variant | 0.94 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1473899 | n.242A>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1473995 | n.338G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
rrl | 1474009 | n.352A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1474012 | n.355C>T | non_coding_transcript_exon_variant | 0.94 | capreomycin | |
linezolid | ||||||
rrl | 1474093 | n.436G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1474099 | n.442G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1474103 | n.446A>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1474140 | n.483C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474151 | n.494C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474181 | n.524C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1474249 | n.592G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474291 | n.635_649delTTCCTCTCCGGAGGA | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1474308 | n.651G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474310 | n.653T>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1474356 | n.699T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1474362 | n.705A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474376 | n.719T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1474639 | n.982G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474794 | n.1137C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474812 | n.1155G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474823 | n.1166C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1474831 | n.1174A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1474904 | n.1247G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1474956 | n.1299C>T | non_coding_transcript_exon_variant | 0.87 | capreomycin | |
linezolid | ||||||
rrl | 1474961 | n.1304T>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1474963 | n.1306G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1474964 | n.1307T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1474970 | n.1313G>A | non_coding_transcript_exon_variant | 0.93 | capreomycin | |
linezolid | ||||||
rrl | 1475006 | n.1349A>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475013 | n.1356G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475088 | n.1431A>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475199 | n.1542G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475206 | n.1549C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475209 | n.1552G>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475213 | n.1556C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475249 | n.1592T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475252 | n.1595C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475266 | n.1609T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475275 | n.1618C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475276 | n.1619T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475291 | n.1634A>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475313 | n.1656G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475315 | n.1658A>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475355 | n.1698C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475369 | n.1712G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475402 | n.1745C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475419 | n.1762C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475483 | n.1826C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475505 | n.1848G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475599 | n.1942A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | Uncertain significance | |||||
rrl | 1475608 | n.1951T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475638 | n.1981C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475642 | n.1985T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475657 | n.2000A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475659 | n.2002G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475761 | n.2104_2106delCGCinsGT | non_coding_transcript_exon_variant | 0.96 | capreomycin | |
linezolid | ||||||
rrl | 1475765 | n.2111delG | non_coding_transcript_exon_variant | 0.96 | capreomycin | |
linezolid | ||||||
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 0.9 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476031 | n.2374C>T | non_coding_transcript_exon_variant | 0.9 | capreomycin | |
linezolid | ||||||
rrl | 1476032 | n.2375C>A | non_coding_transcript_exon_variant | 0.9 | capreomycin | |
linezolid | ||||||
rrl | 1476033 | n.2376T>C | non_coding_transcript_exon_variant | 0.9 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476034 | n.2377C>A | non_coding_transcript_exon_variant | 0.9 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476045 | n.2388G>T | non_coding_transcript_exon_variant | 0.9 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476047 | n.2390G>T | non_coding_transcript_exon_variant | 0.9 | capreomycin | |
linezolid | ||||||
rrl | 1476048 | n.2391G>A | non_coding_transcript_exon_variant | 0.9 | capreomycin | |
linezolid | ||||||
rrl | 1476049 | n.2392C>T | non_coding_transcript_exon_variant | 0.9 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476086 | n.2429G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476089 | n.2432T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1476095 | n.2438C>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1476105 | n.2448_2449delGAinsT | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1476115 | n.2458T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476117 | n.2460G>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476281 | n.2624T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rpsA | 1833838 | c.297G>C | synonymous_variant | 1.0 | pyrazinamide | |
rpsA | 1833841 | c.300C>G | synonymous_variant | 1.0 | pyrazinamide | |
rpsA | 1833847 | c.306C>G | synonymous_variant | 1.0 | pyrazinamide | |
rpsA | 1833856 | c.315A>G | synonymous_variant | 1.0 | pyrazinamide | |
rpsA | 1833874 | c.333T>C | synonymous_variant | 1.0 | pyrazinamide | |
rpsA | 1833886 | c.345C>G | synonymous_variant | 1.0 | pyrazinamide | |
rpsA | 1833928 | c.387G>C | synonymous_variant | 1.0 | pyrazinamide | |
rpsA | 1833940 | c.399C>G | synonymous_variant | 1.0 | pyrazinamide |