Run ID: SRR25827883
Sample name:
Date: 2024-04-15T20:38:53.114836
Number of reads: 6864269
Percentage reads mapped: 99.1
Median coverage: 237.0
Strain: lineage3;lineage4.2.2.2
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.2.2 | Euro-American (Ural) | None | 0.44 |
lineage3 | East-African-Indian | RD750 | 0.55 |
lineage4.2 | Euro-American | None | 0.47 |
lineage4 | Euro-American | None | 0.48 |
lineage4.2.2.2 | Euro-American (Ural) | None | 0.43 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Asp435Tyr | Assoc w R | |
p.Ser450Leu | Assoc w R | |||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
c.707_708delAC | Assoc w R | High-level resistance | ||
ahpC | c.-48G>A | Uncertain significance | Mutation from literature | |
ethambutol | embB | p.Gly406Ala | Assoc w R | |
p.Asp1024Asn | Uncertain significance | Mutation from literature | ||
pyrazinamide | ||||
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Ala90Val | 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 | gyrA | p.Ala90Val | Assoc w R | |
p.Asp94Gly | Assoc w R | |||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | p.Cys253* | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.47 | 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 | 0.51 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | High-level resistance | |||||
rpoB | 761109 | p.Asp435Tyr | missense_variant | 0.55 | rifampicin | Assoc w R | |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.48 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.47 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.47 | isoniazid | Assoc w R | High-level resistance |
katG | 2155403 | c.707_708delAC | frameshift_variant | 0.53 | isoniazid | Assoc w R | High-level resistance |
ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 0.48 | isoniazid | Uncertain significance | Mutation from literature |
embB | 4247730 | p.Gly406Ala | missense_variant | 0.37 | ethambutol | Assoc w R | |
embB | 4249583 | p.Asp1024Asn | missense_variant | 0.5 | ethambutol | Uncertain significance | Mutation from literature |
ethA | 4326715 | p.Cys253* | stop_gained | 0.46 | 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 | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 8025 | p.Asp242His | missense_variant | 0.52 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 8158 | p.Ser286Leu | missense_variant | 0.54 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 8688 | p.Ala463Ser | missense_variant | 0.45 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
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 | 0.6 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 576077 | c.730C>T | synonymous_variant | 0.48 | ethionamide | Not assoc w R - Interim |
isoniazid | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.53 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657425 | p.Gly16Ser | missense_variant | 0.41 | ethionamide | Uncertain significance |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.6 | rifampicin | Not assoc w R |
rpoB | 761489 | c.1683G>A | synonymous_variant | 0.48 | rifampicin | Not assoc w R |
rpoB | 762434 | c.2628T>G | synonymous_variant | 0.52 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.51 | rifampicin | Not assoc w R |
rpoC | 764916 | p.Leu516Pro | missense_variant | 0.48 | rifampicin | Uncertain significance |
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 | 0.53 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpR5 | 779393 | p.Arg135Gln | missense_variant | 0.44 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800204 | c.-605T>C | upstream_gene_variant | 0.46 | linezolid | |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.52 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
Rv1129c | 1254743 | c.-209C>T | upstream_gene_variant | 0.55 | moxifloxacin | |
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
fbiC | 1305050 | p.Thr707Met | missense_variant | 0.43 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1476561 | n.2904C>T | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
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 |
bacA | 2063685 | c.1044G>A | synonymous_variant | 0.48 | streptomycin | Not assoc w R - Interim |
kanamycin | Not assoc w R - Interim | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
bacA | 2063911 | p.Ile273Thr | missense_variant | 0.45 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 0.57 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.61 | 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 | 0.45 | pyrazinamide | Not assoc w R |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.56 | pyrazinamide | |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.53 | isoniazid | Not assoc w R |
ahpC | 2726116 | c.-77T>G | upstream_gene_variant | 0.53 | isoniazid | Uncertain significance |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 0.49 | 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 | |||||
Rv2477c | 2783786 | p.Arg86His | missense_variant | 0.48 | ethambutol | Not assoc w R |
moxifloxacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
Rv2752c | 3066280 | c.-89C>T | upstream_gene_variant | 0.39 | ethambutol | |
moxifloxacin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.41 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
whiB7 | 3568425 | c.255T>G | synonymous_variant | 0.14 | streptomycin | |
amikacin | ||||||
kanamycin | ||||||
whiB7 | 3568428 | c.252A>C | synonymous_variant | 0.18 | streptomycin | |
amikacin | ||||||
kanamycin | ||||||
Rv3236c | 3613591 | c.-475G>A | upstream_gene_variant | 0.58 | pyrazinamide | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
panD | 4044872 | c.-591C>T | upstream_gene_variant | 0.58 | pyrazinamide | |
glpK | 4138622 | c.1134C>T | synonymous_variant | 0.57 | 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 | 0.64 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.19 | ethambutol | |
whiB6 | 4338399 | p.Trp41Cys | missense_variant | 0.5 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.59 | streptomycin | Not assoc w R |
gid | 4408093 | p.Gly37Glu | missense_variant | 0.53 | streptomycin | Uncertain significance |