Run ID: SRR18593215
Sample name:
Date: 2024-10-04T15:21:40.690500
Number of reads: 4559494
Percentage reads mapped: 97.58
Median coverage: 127.0
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.His445Asp | Assoc w R | |
p.Ser450Trp | Assoc w R | |||
isoniazid | katG | p.Ser315Arg | Assoc w R | High-level resistance |
ethambutol | embB | p.Asp354Ala | Assoc w R | |
p.Gln497Lys | Assoc w R | |||
p.Asp1024Asn | Uncertain significance | Mutation from literature | ||
pyrazinamide | ||||
streptomycin | rrs | n.906A>G | Uncertain significance | Mutation from literature |
fluoroquinolones | ||||
moxifloxacin | gyrB | p.Thr500Asn | Uncertain significance | Mutation from literature |
gyrA | p.Asp89Asn | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |
p.Asp94Gly | Assoc w R | High-level resistance | ||
ofloxacin | ||||
levofloxacin | gyrB | p.Thr500Asn | Uncertain significance | Mutation from literature |
gyrA | p.Asp89Asn | Assoc w R | ||
p.Asp94Gly | Assoc w R | |||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | tlyA | c.126_127dupGG | Assoc w R | |
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | c.788_798delTGTTCCTGAGC | Assoc w R | |
c.752dupG | Assoc w R | |||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrB | 6738 | p.Thr500Asn | missense_variant | 0.73 | levofloxacin | Uncertain significance | Mutation from literature |
moxifloxacin | Uncertain significance | Mutation from literature | |||||
gyrA | 7566 | p.Asp89Asn | missense_variant | 0.89 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.11 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | High-level resistance | |||||
rpoB | 761139 | p.His445Asp | missense_variant | 0.88 | rifampicin | Assoc w R | |
rpoB | 761155 | p.Ser450Trp | missense_variant | 0.12 | rifampicin | Assoc w R | |
rrs | 1472751 | n.906A>G | non_coding_transcript_exon_variant | 0.13 | streptomycin | Uncertain significance | Mutation from literature |
tlyA | 1918064 | c.126_127dupGG | frameshift_variant | 0.14 | capreomycin | Assoc w R | |
katG | 2155169 | p.Ser315Arg | missense_variant | 0.83 | isoniazid | Assoc w R | High-level resistance |
embB | 4247574 | p.Asp354Ala | missense_variant | 0.11 | ethambutol | Assoc w R | |
embB | 4248002 | p.Gln497Lys | missense_variant | 0.78 | ethambutol | Assoc w R | |
embB | 4249583 | p.Asp1024Asn | missense_variant | 0.86 | ethambutol | Uncertain significance | Mutation from literature |
ethA | 4326675 | c.788_798delTGTTCCTGAGC | frameshift_variant | 0.85 | ethionamide | Assoc w R | |
ethA | 4326721 | c.752dupG | frameshift_variant | 0.15 | ethionamide | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6091 | c.852G>A | synonymous_variant | 0.96 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
mshA | 574518 | c.-830A>G | upstream_gene_variant | 0.98 | isoniazid | |
ethionamide | ||||||
rpoB | 761231 | c.1425C>T | synonymous_variant | 1.0 | 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 |
Rv1129c | 1253847 | p.Ala230Thr | missense_variant | 0.89 | 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 | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.98 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
inhA | 1674283 | p.Val28Leu | missense_variant | 0.98 | isoniazid | Uncertain significance |
ethionamide | ||||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 0.99 | capreomycin | Not assoc w R |
katG | 2155627 | p.Ala162Glu | missense_variant | 0.11 | isoniazid | Uncertain significance |
katG | 2156419 | c.-308C>A | upstream_gene_variant | 0.84 | isoniazid | |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
pncA | 2288832 | p.His137Leu | missense_variant | 0.12 | pyrazinamide | |
pncA | 2289040 | c.187_201dupGACTATTCCTCGTCG | conservative_inframe_insertion | 0.76 | pyrazinamide | |
ahpC | 2726142 | c.-51G>A | upstream_gene_variant | 0.17 | isoniazid | Uncertain significance |
Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 0.96 | capreomycin | |
Rv2752c | 3065938 | p.Asp85Gly | missense_variant | 0.15 | levofloxacin | Uncertain significance |
moxifloxacin | ||||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
ald | 3086966 | p.Asp49Glu | missense_variant | 0.98 | cycloserine | |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 0.98 | ethionamide | Uncertain significance |
Rv3236c | 3612047 | p.Ala357Val | missense_variant | 0.99 | pyrazinamide | Uncertain significance |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4326505 | c.969C>G | synonymous_variant | 0.95 | ethionamide | Not assoc w R - Interim |
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 | 4408139 | p.Tyr22Asn | missense_variant | 0.89 | streptomycin | Uncertain significance |