Run ID: SRR26159063
Sample name:
Date: 2024-04-16T01:47:44.490928
Number of reads: 429093
Percentage reads mapped: 99.4
Median coverage: 0.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: RR-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 | rpoB | c.1327_1329delTTGinsCC | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
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 |
---|---|---|---|---|---|---|---|
rpoB | 761133 | c.1327_1329delTTGinsCC | frameshift_variant&missense_variant | 0.93 | rifampicin | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 6565 | c.-737G>C | upstream_gene_variant | 0.91 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 6571 | c.-731T>C | upstream_gene_variant | 0.97 | levofloxacin | |
moxifloxacin | ||||||
rpoB | 760961 | c.1155C>T | synonymous_variant | 0.93 | rifampicin | |
rpoB | 760991 | c.1185G>C | synonymous_variant | 0.93 | rifampicin | |
rpoB | 761015 | c.1209G>C | synonymous_variant | 0.94 | rifampicin | Not assoc w R - Interim |
rpoB | 761027 | c.1221A>G | synonymous_variant | 0.94 | rifampicin | Not assoc w R - Interim |
rpoB | 761057 | c.1251G>C | synonymous_variant | 0.95 | rifampicin | Not assoc w R - Interim |
rpoB | 761060 | c.1254C>T | synonymous_variant | 0.93 | rifampicin | Not assoc w R - Interim |
rpoB | 761063 | c.1257C>G | synonymous_variant | 0.94 | rifampicin | Not assoc w R - Interim |
rpoB | 761094 | c.1288C>T | synonymous_variant | 0.9 | rifampicin | Not assoc w R - Interim |
rpoB | 761097 | c.1291_1293delAGCinsTCG | synonymous_variant | 0.9 | rifampicin | |
rpoB | 761102 | c.1296A>G | synonymous_variant | 0.92 | rifampicin | |
rpoB | 761132 | c.1326G>T | synonymous_variant | 0.92 | rifampicin | Not assoc w R - Interim |
rpoB | 761150 | c.1344A>C | synonymous_variant | 0.95 | rifampicin | Not assoc w R - Interim |
rpoB | 761171 | c.1365C>T | synonymous_variant | 0.91 | rifampicin | Not assoc w R - Interim |
rpoB | 761180 | c.1374A>C | synonymous_variant | 0.96 | rifampicin | Not assoc w R - Interim |
rpoB | 761189 | c.1383T>G | synonymous_variant | 0.96 | rifampicin | |
rpoB | 761192 | c.1386C>G | synonymous_variant | 0.95 | rifampicin | |
rpoB | 761195 | c.1389G>C | synonymous_variant | 0.96 | rifampicin | Not assoc w R - Interim |
rpoB | 761234 | c.1428G>C | synonymous_variant | 0.99 | rifampicin | Not assoc w R - Interim |
rpoB | 761249 | c.1443A>G | synonymous_variant | 0.99 | rifampicin | Not assoc w R - Interim |
rpoB | 761255 | c.1449T>G | synonymous_variant | 0.99 | rifampicin | Not assoc w R - Interim |
rpoB | 761261 | c.1455G>T | synonymous_variant | 0.99 | rifampicin | Not assoc w R - Interim |
rpoB | 761286 | c.1480C>T | synonymous_variant | 1.0 | rifampicin | |
rpoB | 761300 | c.1494G>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoB | 761327 | c.1521A>G | synonymous_variant | 0.99 | rifampicin | Not assoc w R - Interim |
rpoB | 761345 | c.1539G>C | synonymous_variant | 0.99 | rifampicin | |
rpoB | 761346 | p.Val514Ile | missense_variant | 0.99 | rifampicin | |
rpoB | 761354 | c.1548C>T | synonymous_variant | 0.99 | rifampicin | |
rrs | 1472286 | n.441C>G | non_coding_transcript_exon_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472289 | n.444T>G | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472290 | n.445C>G | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472297 | n.453_465delGTCCGGGTTCTCT | non_coding_transcript_exon_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472313 | n.468delGinsCA | non_coding_transcript_exon_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472315 | n.470T>G | non_coding_transcript_exon_variant | 1.0 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472324 | n.479G>C | non_coding_transcript_exon_variant | 0.99 | streptomycin | Uncertain significance |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472325 | n.480G>C | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472328 | n.483G>C | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472969 | n.1124A>G | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472970 | n.1125C>G | non_coding_transcript_exon_variant | 1.0 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472977 | n.1132G>C | non_coding_transcript_exon_variant | 1.0 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472978 | n.1133T>C | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473104 | n.1259C>T | non_coding_transcript_exon_variant | 0.96 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473105 | n.1260G>A | non_coding_transcript_exon_variant | 0.98 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473123 | n.1278delAinsTT | non_coding_transcript_exon_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1473290 | n.1445C>T | non_coding_transcript_exon_variant | 1.0 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1473417 | n.-241C>T | upstream_gene_variant | 0.99 | capreomycin | |
linezolid | ||||||
rrl | 1473421 | n.-237G>A | upstream_gene_variant | 0.99 | capreomycin | |
linezolid | ||||||
rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476033 | n.2376T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476035 | n.2378G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
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 | 1476103 | n.2446C>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476105 | n.2448G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476106 | n.2449A>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476110 | n.2453G>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
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 | 1476118 | n.2461G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476131 | n.2474C>T | non_coding_transcript_exon_variant | 0.99 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476214 | n.2557G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476215 | n.2558C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476245 | n.2588C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476583 | n.2926G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476584 | n.2927C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476597 | n.2940G>A | non_coding_transcript_exon_variant | 0.98 | capreomycin | Uncertain significance |
linezolid |