Run ID: ERR4817847
Sample name:
Date: 2024-10-05T08:38:30.466757
Number of reads: 2502312
Percentage reads mapped: 93.18
Median coverage: 74.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.97 |
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 | 412 | p.Ala138Thr | missense_variant | 0.99 | isoniazid | Uncertain significance |
gyrB | 5524 | c.285C>A | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.13 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13442 | p.Leu39Phe | missense_variant | 1.0 | isoniazid | Uncertain significance |
rpoB | 760101 | c.295T>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoB | 760112 | c.306T>C | synonymous_variant | 0.13 | rifampicin | |
rpoB | 760121 | c.315T>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoB | 760181 | c.375T>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoB | 760184 | c.378A>G | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoB | 760196 | c.390C>G | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoB | 762101 | c.2295C>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoB | 762114 | p.Ile770Val | missense_variant | 0.13 | rifampicin | Uncertain significance |
rpoB | 762131 | c.2325C>G | synonymous_variant | 0.13 | rifampicin | |
rpoB | 762140 | c.2334G>C | synonymous_variant | 0.13 | rifampicin | |
rpoB | 762149 | c.2343G>C | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
rpoB | 762167 | c.2361T>C | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
rpoB | 762176 | c.2370T>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoB | 763085 | c.3279C>G | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoB | 763115 | c.3309T>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 764497 | c.1128A>G | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
rpoC | 766312 | c.2943T>G | synonymous_variant | 0.12 | rifampicin | |
rpoC | 766345 | c.2976T>C | synonymous_variant | 0.17 | rifampicin | |
rpoC | 766348 | c.2979A>G | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoC | 766363 | c.2994G>C | synonymous_variant | 0.16 | rifampicin | |
rpoC | 766381 | c.3012C>T | synonymous_variant | 0.19 | rifampicin | |
rpoC | 766384 | c.3015A>G | synonymous_variant | 0.18 | rifampicin | |
rpoC | 766390 | c.3021C>T | synonymous_variant | 0.12 | rifampicin | |
rpoC | 766426 | c.3057C>T | synonymous_variant | 0.15 | rifampicin | |
mmpL5 | 775639 | p.Ile948Val | 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 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473290 | n.1445C>T | non_coding_transcript_exon_variant | 0.21 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 0.96 | capreomycin | |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 0.93 | ethionamide | Uncertain significance |
clpC1 | 4038878 | c.1827A>G | synonymous_variant | 0.16 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4038908 | c.1797C>G | synonymous_variant | 0.13 | pyrazinamide | |
clpC1 | 4038956 | c.1749T>C | synonymous_variant | 0.13 | pyrazinamide | |
clpC1 | 4038965 | c.1740T>C | synonymous_variant | 0.13 | pyrazinamide | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4247470 | c.957T>C | synonymous_variant | 0.16 | ethambutol | |
embB | 4247512 | c.999T>C | synonymous_variant | 0.13 | ethambutol | |
embB | 4249354 | c.2841G>C | synonymous_variant | 0.98 | ethambutol | Not assoc w R - Interim |
whiB6 | 4338590 | c.-69A>T | upstream_gene_variant | 0.97 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R |