Run ID: SRR28888061
Sample name:
Date: 2024-05-22T15:41:19.852885
Number of reads: 4455918
Percentage reads mapped: 99.64
Median coverage: 139.0
Strain: lineage2.2.1
Spoligotype:
Drug-resistance: XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 1.0 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Leu430Pro | Assoc w R | |
p.Asp435Gly | Assoc w R - Interim | |||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Gln497Arg | Assoc w R | |
pyrazinamide | pncA | p.Asp12Asn | Assoc w R - Interim | |
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.Asp94Ala | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | ||
ofloxacin | ||||
levofloxacin | gyrA | p.Ala90Val | Assoc w R | |
p.Asp94Ala | Assoc w R | |||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | tlyA | c.397dupC | Assoc w R | |
kanamycin | eis | c.-10G>A | Assoc w R | Can only confer resistance if genetically linked to a functional Eis |
cycloserine | ||||
ethionamide | ethA | c.703delT | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid | rplC | p.Cys154Arg | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.98 | 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 | 0.99 | 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 | 761095 | p.Leu430Pro | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpoB | 761110 | p.Asp435Gly | missense_variant | 1.0 | rifampicin | Assoc w R - Interim | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
rplC | 801268 | p.Cys154Arg | missense_variant | 0.82 | linezolid | Assoc w R | |
tlyA | 1918335 | c.397dupC | frameshift_variant | 0.99 | capreomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289208 | p.Asp12Asn | missense_variant | 1.0 | pyrazinamide | Assoc w R - Interim | |
eis | 2715342 | c.-10G>A | upstream_gene_variant | 1.0 | kanamycin | Assoc w R | Can only confer resistance if genetically linked to a functional Eis |
embB | 4248003 | p.Gln497Arg | missense_variant | 1.0 | ethambutol | Assoc w R | |
ethA | 4326770 | c.703delT | frameshift_variant | 1.0 | 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 | 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 | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 | 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 | 1.0 | ethionamide | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 0.99 | 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 | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R | |||||
mmpR5 | 779414 | p.Leu142Arg | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800403 | c.-406_-405insGGTCCAGAAGGA | upstream_gene_variant | 0.74 | linezolid | |
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 | |||||
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 | streptomycin | Uncertain significance |
isoniazid | Uncertain significance | |||||
pyrazinamide | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 | 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 |
ndh | 2102417 | p.Ala209Val | missense_variant | 1.0 | ethionamide | Uncertain significance |
delamanid | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
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 | |||||
Rv2752c | 3065174 | c.1015_1017delTCG | conservative_inframe_deletion | 1.0 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
thyX | 3067954 | c.-9G>A | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
thyA | 3074080 | p.Ser131Leu | missense_variant | 1.0 | para-aminosalicylic_acid | |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3087648 | c.830_831dupGC | frameshift_variant | 0.99 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 | 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 | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243346 | c.114A>G | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.2 | ethambutol | |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 | ethambutol | Not assoc w R |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
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 | 1.0 | streptomycin | Not assoc w R |