Run ID: SRR29273690
Sample name:
Date: 2025-02-11T14:01:52.415691
Number of reads: 2870826
Percentage reads mapped: 99.7
Median coverage: 91.0
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.Ser450Trp | Assoc w R | |
isoniazid | ||||
ethambutol | embB | p.Met306Ile | Assoc w R | |
p.Glu504Asp | Uncertain significance | Mutation from literature | ||
pyrazinamide | pncA | c.223_230dupGGTACTCC | Assoc w R | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94Gly | Assoc w R | High-level resistance |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94Gly | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | rrs | n.1401A>G | Assoc w R | |
capreomycin | rrs | n.1401A>G | Assoc w R | |
kanamycin | rrs | n.1401A>G | Assoc w R | |
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | High-level resistance | |||||
rpoB | 761155 | p.Ser450Trp | missense_variant | 1.0 | rifampicin | Assoc w R | |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | amikacin | Assoc w R | |
capreomycin | Assoc w R | ||||||
kanamycin | Assoc w R | ||||||
pncA | 2289011 | c.223_230dupGGTACTCC | frameshift_variant | 1.0 | pyrazinamide | Assoc w R | |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol | Assoc w R | |
embB | 4248025 | p.Glu504Asp | missense_variant | 0.95 | 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 | |||||
Rv0565c | 656265 | c.1204_1205delAC | frameshift_variant | 1.0 | ethionamide | Uncertain significance |
nusG | 734658 | c.405A>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
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 |
Rv1129c | 1254197 | p.Met113Thr | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
katG | 2155258 | p.Gly285Val | missense_variant | 1.0 | isoniazid | Uncertain significance |
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 | 1.0 | capreomycin | |
Rv2752c | 3064966 | p.Leu409Pro | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
ethambutol | ||||||
ald | 3086999 | c.180C>G | synonymous_variant | 1.0 | cycloserine | |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 | ethionamide | Uncertain significance |
Rv3236c | 3613636 | c.-520A>G | upstream_gene_variant | 1.0 | pyrazinamide | Not assoc w R |
alr | 3840463 | p.Arg320Trp | missense_variant | 1.0 | cycloserine | |
clpC1 | 4039729 | p.Asp326Asn | missense_variant | 0.98 | pyrazinamide | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4326857 | p.Gln206Arg | missense_variant | 1.0 | ethionamide | |
ethA | 4327461 | p.Leu5Phe | missense_variant | 1.0 | ethionamide | 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 | |||||
gid | 4407712 | p.Gly164Val | missense_variant | 1.0 | streptomycin | Uncertain significance |