Run ID: SRR9738484
Sample name:
Date: 2024-04-15T03:44:11.026458
Number of reads: 2430270
Percentage reads mapped: 96.69
Median coverage: 60.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | RD219 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Met306Val | Assoc w R | |
pyrazinamide | pncA | p.Ala171Thr | Uncertain significance | Mutation from literature |
streptomycin | rrs | n.878G>A | Assoc w R - Interim | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | eis | c.-10G>A | Assoc w R | Can only confer resistance if genetically linked to a functional Eis |
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
rrs | 1472723 | n.878G>A | non_coding_transcript_exon_variant | 0.99 | streptomycin | Assoc w R - Interim | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288731 | p.Ala171Thr | missense_variant | 1.0 | pyrazinamide | Uncertain significance | Mutation from literature |
eis | 2715342 | c.-10G>A | upstream_gene_variant | 1.0 | kanamycin | Assoc w R | Can only confer resistance if genetically linked to a functional Eis |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol | Assoc w R |
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 | |||||
rpoC | 764705 | p.Leu446Val | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoC | 765926 | p.Thr853Ala | missense_variant | 1.0 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800202 | c.-607G>C | upstream_gene_variant | 1.0 | linezolid | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
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 |
bacA | 2063664 | c.1065T>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R - Interim |
kanamycin | Not assoc w R - Interim | |||||
capreomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
PPE35 | 2170035 | p.Val193Ala | missense_variant | 0.98 | pyrazinamide | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
ribD | 2986828 | c.-11C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
Rv2680 | 2996133 | p.Arg10Gln | missense_variant | 0.22 | capreomycin | |
Rv2681 | 2997537 | p.Asp267Tyr | missense_variant | 1.0 | capreomycin | Uncertain significance |
Rv2752c | 3067180 | c.-989C>A | upstream_gene_variant | 1.0 | ethambutol | |
moxifloxacin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
thyA | 3074172 | c.300G>T | synonymous_variant | 1.0 | para-aminosalicylic_acid | |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 | ethionamide | Uncertain significance |
fbiA | 3640472 | c.-71G>A | upstream_gene_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
glpK | 4139275 | p.Gly161Arg | missense_variant | 0.85 | ethambutol | Uncertain significance |
moxifloxacin | ||||||
streptomycin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R |