Run ID: SRR7592364
Sample name:
Date: 2024-03-26T12:56:34.704592
Number of reads: 3816931
Percentage reads mapped: 99.97
Median coverage: 97.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: Pre-XDR-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.Gln432Pro | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Met306Val | Assoc w R | |
pyrazinamide | pncA | p.Val180Gly | Assoc w R | |
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrB | p.Asn499Lys | Uncertain significance | Mutation from literature |
ofloxacin | ||||
levofloxacin | gyrB | p.Asn499Lys | Uncertain significance | Mutation from literature |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | eis | c.-12C>T | Assoc w R | |
cycloserine | alr | p.Met343Thr | Mutation from literature | |
ethionamide | ethA | c.752dupG | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrB | 6736 | p.Asn499Lys | missense_variant | 1.0 | levofloxacin | Uncertain significance | Mutation from literature |
moxifloxacin | Uncertain significance | Mutation from literature | |||||
rpoB | 761101 | p.Gln432Pro | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288703 | p.Val180Gly | missense_variant | 0.98 | pyrazinamide | Assoc w R | |
eis | 2715344 | c.-12C>T | upstream_gene_variant | 1.0 | kanamycin | Assoc w R | |
alr | 3840393 | p.Met343Thr | missense_variant | 1.0 | cycloserine | Mutation from literature | |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol | Assoc w R | |
ethA | 4326721 | c.752dupG | frameshift_variant | 1.0 | ethionamide | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1524 | c.1524G>T | stop_lost&splice_region_variant | 1.0 | isoniazid | Uncertain significance |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
mshA | 575599 | c.254_255dupAG | frameshift_variant | 0.96 | ethionamide | Uncertain significance |
isoniazid | Uncertain significance | |||||
rpoC | 764817 | p.Val483Gly | missense_variant | 0.99 | 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 |
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 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.17 | pyrazinamide | |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.17 | pyrazinamide | |
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 | |
fbiA | 3640974 | c.432T>G | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
embC | 4241699 | p.Met613Val | missense_variant | 1.0 | ethambutol | Uncertain significance |
embC | 4242643 | c.2781C>T | synonymous_variant | 0.99 | ethambutol | Not assoc w R |
whiB6 | 4338234 | c.288A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R - Interim |
amikacin | Not assoc w R - Interim | |||||
kanamycin | 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 |