Run ID: SRR28045567
Sample name:
Date: 2024-05-22T11:00:42.957759
Number of reads: 15680701
Percentage reads mapped: 99.57
Median coverage: 438.0
Strain: lineage3
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Arg104Gln | Uncertain significance | Mutation from literature |
ethambutol | embA | c.-12C>T | Uncertain significance | Mutation from literature |
embB | p.Gly406Cys | Assoc w R | ||
pyrazinamide | pncA | c.475dupC | Assoc w R | |
streptomycin | rpsL | p.Lys88Thr | Uncertain significance | Mutation from literature |
fluoroquinolones | ||||
moxifloxacin | gyrB | p.Asp461Asn | Assoc w R - Interim | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
gyrA | p.Asp94Ala | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |
ofloxacin | ||||
levofloxacin | gyrB | p.Asp461Asn | Assoc w R | |
gyrA | p.Asp94Ala | Assoc w R | ||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrB | 6620 | p.Asp461Asn | missense_variant | 1.0 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R - Interim | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
gyrA | 7582 | p.Asp94Ala | missense_variant | 1.0 | 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) | |||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpsL | 781822 | p.Lys88Thr | missense_variant | 1.0 | streptomycin | Uncertain significance | Mutation from literature |
katG | 2155801 | p.Arg104Gln | missense_variant | 1.0 | isoniazid | Uncertain significance | Mutation from literature |
pncA | 2288766 | c.475dupC | frameshift_variant | 1.0 | pyrazinamide | Assoc w R | |
embA | 4243221 | c.-12C>T | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance | Mutation from literature |
embB | 4247729 | p.Gly406Cys | 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 | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 8056 | p.Arg252Leu | missense_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Uncertain significance | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657346 | p.Arg42Thr | missense_variant | 1.0 | ethionamide | |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
rpoB | 762434 | c.2628T>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776100 | p.Thr794Ile | 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 |
Rv1129c | 1253471 | p.His355Arg | missense_variant | 1.0 | moxifloxacin | Uncertain significance |
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | 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 | |||||
pncA | 2289047 | c.195C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 | pyrazinamide | |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 | isoniazid | Not assoc w R |
ahpC | 2726116 | c.-77T>A | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3086946 | c.128dupC | frameshift_variant | 1.0 | cycloserine | |
Rv3083 | 3448768 | p.Ala89Thr | missense_variant | 1.0 | ethionamide | |
Rv3236c | 3613307 | c.-191G>T | upstream_gene_variant | 1.0 | pyrazinamide | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
rpoA | 3878619 | c.-112A>C | upstream_gene_variant | 0.13 | rifampicin | |
panD | 4044872 | c.-591C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
glpK | 4138622 | c.1134C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243447 | p.Ile72Thr | missense_variant | 1.0 | ethambutol | |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.24 | ethambutol | |
embB | 4247033 | p.Ser174Arg | missense_variant | 0.13 | ethambutol | |
ubiA | 4269294 | p.Met180Ile | missense_variant | 1.0 | ethambutol | Uncertain significance |
ethA | 4326278 | p.Ser399Leu | missense_variant | 1.0 | ethionamide | Uncertain significance |
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |