Run ID: ERR688043
Sample name:
Date: 2024-06-18T07:37:18.162077
Number of reads: 25602700
Percentage reads mapped: 99.66
Median coverage: 545.0
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 | 0.96 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
katG | p.Ser315Thr | Assoc w R | High-level resistance | |
ethambutol | embB | p.Met306Ile | Assoc w R | |
p.Gly406Asp | Assoc w R | |||
pyrazinamide | pncA | p.Gly97Ser | Assoc w R | |
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrB | p.Ser447Phe | Assoc w R - Interim | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ofloxacin | ||||
levofloxacin | gyrB | p.Ser447Phe | Assoc w R - Interim | |
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 | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
ethA | c.299delT | Assoc w R | ||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrB | 6579 | p.Ser447Phe | missense_variant | 0.97 | levofloxacin | Assoc w R - Interim | |
moxifloxacin | Assoc w R - Interim | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.96 | streptomycin | Assoc w R | |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.97 | kanamycin | Assoc w R | |
capreomycin | Assoc w R | ||||||
amikacin | Assoc w R | ||||||
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.96 | ethionamide | Assoc w R | Alias fabG1_c.-15C>T |
isoniazid | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288953 | p.Gly97Ser | missense_variant | 0.96 | pyrazinamide | Assoc w R | |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol | Assoc w R | |
embB | 4247730 | p.Gly406Asp | missense_variant | 0.95 | ethambutol | Assoc w R | |
ethA | 4327174 | c.299delT | frameshift_variant | 0.94 | ethionamide | 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 | |||||
Rv0010c | 13636 | c.-78A>G | upstream_gene_variant | 0.95 | isoniazid | Uncertain significance |
Rv0565c | 656265 | c.1204_1205delAC | frameshift_variant | 0.95 | ethionamide | Uncertain significance |
rpoC | 764616 | p.Asn416Ser | missense_variant | 0.96 | rifampicin | Uncertain significance |
rpoC | 765331 | c.1962C>T | synonymous_variant | 0.96 | rifampicin | Not assoc w R - Interim |
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 | 0.95 | 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 | 0.95 | 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 | 0.94 | capreomycin | |
ald | 3087759 | c.942delC | frameshift_variant | 0.87 | cycloserine | |
ald | 3087805 | p.Trp329* | stop_gained | 0.11 | cycloserine | |
Rv3083 | 3448497 | c.-7T>A | upstream_gene_variant | 0.24 | ethionamide | |
Rv3083 | 3448500 | c.-4A>G | upstream_gene_variant | 0.19 | ethionamide | |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 0.96 | ethionamide | 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 |