Run ID: SRR3105742
Sample name:
Date: 2024-04-16T08:31:04.208902
Number of reads: 1471274
Percentage reads mapped: 98.44
Median coverage: 28.0
Strain: lineage2.2.1;lineage3
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 0.44 |
lineage2 | East-Asian | RD105 | 0.55 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.57 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.61 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Asp435Tyr | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embA | c.-16C>T | Uncertain significance | Mutation from literature |
embB | p.Met306Val | Assoc w R | ||
p.Pro404Ser | Uncertain significance | Mutation from literature | ||
pyrazinamide | pncA | c.391dupG | Assoc w R | |
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
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.Ala90Val | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |
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.Ala90Val | Assoc w R | ||
p.Asp94Ala | Assoc w R | |||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | c.926dupA | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrB | 6620 | p.Asp461Asn | missense_variant | 0.38 | 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 | 7570 | p.Ala90Val | missense_variant | 0.48 | 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.Asp94Ala | missense_variant | 0.52 | moxifloxacin | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
levofloxacin | Assoc w R | ||||||
rpoB | 761109 | p.Asp435Tyr | missense_variant | 0.65 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.79 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.7 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288850 | c.391dupG | frameshift_variant | 0.3 | pyrazinamide | Assoc w R | |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 0.43 | ethambutol | Uncertain significance | Mutation from literature |
embB | 4247429 | p.Met306Val | missense_variant | 0.47 | ethambutol | Assoc w R | |
embB | 4247723 | p.Pro404Ser | missense_variant | 0.61 | ethambutol | Uncertain significance | Mutation from literature |
ethA | 4326547 | c.926dupA | frameshift_variant | 0.5 | ethionamide | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 845 | p.Ile282Thr | missense_variant | 0.59 | isoniazid | Uncertain significance |
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 | 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 | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.47 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.8 | ethionamide | Uncertain significance |
Rv0565c | 657263 | c.207delT | frameshift_variant | 0.39 | ethionamide | Uncertain significance |
rpoB | 760321 | p.Gln172Arg | missense_variant | 0.4 | rifampicin | Uncertain significance |
rpoB | 762434 | c.2628T>G | synonymous_variant | 0.42 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.95 | 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 | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.53 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R | |||||
mmpR5 | 779048 | p.Val20Ala | missense_variant | 0.42 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.71 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
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 | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.48 | pyrazinamide | Not assoc w R - Interim |
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 |
katG | 2155653 | p.Lys153Asn | missense_variant | 0.46 | isoniazid | Uncertain significance |
katG | 2155724 | p.Ala130Thr | missense_variant | 0.45 | isoniazid | Uncertain significance |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.94 | 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 | |||||
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.48 | isoniazid | Not assoc w R |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 0.33 | 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 | |||||
pepQ | 2860572 | c.-154G>A | upstream_gene_variant | 0.45 | clofazimine | |
bedaquiline | ||||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.97 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.63 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.57 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
panD | 4044872 | c.-591C>T | upstream_gene_variant | 0.48 | pyrazinamide | |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.38 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.61 | ethambutol | Not assoc w R |
embB | 4249757 | p.Thr1082Ala | missense_variant | 0.5 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.48 | ethambutol | Not assoc w R |
aftB | 4269564 | c.-728G>A | upstream_gene_variant | 0.53 | ethambutol | |
ethA | 4327132 | p.Asn114Lys | missense_variant | 0.36 | ethionamide | |
whiB6 | 4338286 | c.235delG | frameshift_variant | 0.26 | 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 | 1.0 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.45 | streptomycin | Not assoc w R |
gid | 4408018 | p.Gly62Val | missense_variant | 0.57 | streptomycin | Uncertain significance |
gid | 4408168 | p.Phe12Cys | missense_variant | 0.4 | streptomycin | Uncertain significance |