Run ID: SRR25827330
Sample name:
Date: 2024-10-04T14:05:10.019491
Number of reads: 2382639
Percentage reads mapped: 49.85
Median coverage: 71.0
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.Gly406Asp | Assoc w R | |
pyrazinamide | ||||
streptomycin | rpsL | p.Lys43Arg | 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 | 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 |
embB | 4247730 | p.Gly406Asp | 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 | |||||
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 |
rpoC | 766691 | p.Gly1108Ser | missense_variant | 0.81 | rifampicin | Uncertain significance |
rpoC | 766945 | c.3576A>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 766963 | c.3594T>C | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoC | 766972 | c.3603G>C | synonymous_variant | 0.2 | rifampicin | |
rpoC | 766975 | c.3606C>T | synonymous_variant | 0.2 | rifampicin | Not assoc w R - Interim |
rpoC | 766996 | c.3627C>T | synonymous_variant | 0.21 | rifampicin | Not assoc w R - Interim |
rpoC | 767002 | c.3633G>C | synonymous_variant | 0.23 | rifampicin | Not assoc w R - Interim |
rpoC | 767033 | c.3664_3666delTCGinsAGT | synonymous_variant | 0.22 | rifampicin | |
rpoC | 767059 | c.3690T>G | synonymous_variant | 0.28 | rifampicin | Not assoc w R - Interim |
rpoC | 767062 | c.3693C>A | synonymous_variant | 0.27 | rifampicin | |
rpoC | 767098 | c.3729T>C | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoC | 767119 | c.3750A>G | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
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 | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
rpsA | 1834303 | c.762T>G | synonymous_variant | 0.12 | pyrazinamide | |
rpsA | 1834306 | c.765T>C | synonymous_variant | 0.14 | pyrazinamide | |
rpsA | 1834336 | c.795C>G | synonymous_variant | 0.2 | pyrazinamide | |
rpsA | 1834339 | c.798C>T | synonymous_variant | 0.2 | pyrazinamide | |
rpsA | 1834348 | c.807T>C | synonymous_variant | 0.21 | pyrazinamide | Not assoc w R - Interim |
rpsA | 1834366 | c.825A>G | synonymous_variant | 0.23 | pyrazinamide | Not assoc w R - Interim |
rpsA | 1834369 | c.828C>G | synonymous_variant | 0.23 | pyrazinamide | |
rpsA | 1834375 | c.834G>A | synonymous_variant | 0.23 | pyrazinamide | |
rpsA | 1834396 | c.855G>C | synonymous_variant | 0.2 | pyrazinamide | |
rpsA | 1834411 | c.870T>C | synonymous_variant | 0.15 | pyrazinamide | |
rpsA | 1834417 | c.876G>C | synonymous_variant | 0.14 | pyrazinamide | |
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 | |||||
ahpC | 2726510 | p.Leu106Phe | missense_variant | 1.0 | isoniazid | Uncertain significance |
Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 1.0 | capreomycin | |
Rv3236c | 3613636 | c.-520A>G | upstream_gene_variant | 1.0 | pyrazinamide | Not assoc w R |
clpC1 | 4039729 | p.Asp326Asn | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4326977 | p.His166Pro | missense_variant | 0.79 | ethionamide | Uncertain significance |
ethA | 4327386 | p.Lys30Glu | missense_variant | 0.25 | ethionamide | |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R |