Run ID: SRR1173412
Sample name:
Date: 2024-04-16T05:34:46.900310
Number of reads: 3002319
Percentage reads mapped: 97.6
Median coverage: 65.0
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.Gln525Pro | Uncertain significance | Mutation from literature |
ethambutol | embA | c.-12C>T | Uncertain significance | Mutation from literature |
embB | p.Glu504Asp | Uncertain significance | Mutation from literature | |
pyrazinamide | pncA | p.Val131Phe | Assoc w R - Interim | |
streptomycin | rpsL | p.Lys88Arg | Assoc w R | |
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 | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpsL | 781822 | p.Lys88Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
katG | 2154538 | p.Gln525Pro | missense_variant | 0.98 | isoniazid | Uncertain significance | Mutation from literature |
pncA | 2288851 | p.Val131Phe | missense_variant | 0.89 | pyrazinamide | Assoc w R - Interim | |
embA | 4243221 | c.-12C>T | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance | Mutation from literature |
embB | 4248025 | p.Glu504Asp | missense_variant | 1.0 | ethambutol | Uncertain significance | Mutation from literature |
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 | |||||
Rv0010c | 13705 | c.-147G>A | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
rpoB | 760975 | p.Met390Thr | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoC | 765920 | p.Ile851Val | missense_variant | 0.87 | 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 |
Rv1129c | 1254598 | c.-65dupA | upstream_gene_variant | 0.99 | moxifloxacin | |
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
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 | |||||
rrl | 1475090 | n.1433A>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.98 | pyrazinamide | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 1.0 | capreomycin | |
ald | 3086767 | c.-53A>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 | ethionamide | Uncertain significance |
glpK | 4138552 | p.Cys402Gly | missense_variant | 0.83 | ethambutol | |
moxifloxacin | ||||||
streptomycin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
aftB | 4267715 | c.1122G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R |