Run ID: ERR11243546
Sample name:
Date: 21-04-2023 21:28:17
Number of reads: 609453
Percentage reads mapped: 99.6
Strain: lineage2.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00), rpoB p.Glu761Asp (1.00) |
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Asp354Ala (1.00) |
Pyrazinamide | R | pncA p.Tyr103His (1.00) |
Streptomycin | R | rrs n.517C>T (1.00) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | R | eis c.-37G>T (1.00) |
Cycloserine | ||
Ethionamide | R | ethA c.-7T>C (1.00) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 1.0 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpoB | 762089 | p.Glu761Asp | missense_variant | 1.0 | rifampicin |
rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288935 | p.Tyr103His | missense_variant | 1.0 | pyrazinamide |
eis | 2715369 | c.-37G>T | upstream_gene_variant | 1.0 | kanamycin |
embB | 4247574 | p.Asp354Ala | missense_variant | 1.0 | ethambutol |
ethA | 4327480 | c.-7T>C | upstream_gene_variant | 1.0 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6109 | c.870G>C | synonymous_variant | 0.12 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 620408 | p.Pro173Leu | missense_variant | 0.17 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpS5 | 778604 | p.Pro101His | missense_variant | 0.13 |
mmpR5 | 779425 | p.Met146Leu | missense_variant | 0.25 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1475462 | n.1809delA | non_coding_transcript_exon_variant | 0.13 |
inhA | 1674908 | p.Thr236Met | missense_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ribD | 2986987 | p.Asp50Val | missense_variant | 0.12 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3086793 | c.-27A>G | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474534 | c.528C>T | synonymous_variant | 0.11 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
alr | 3841280 | c.141C>T | synonymous_variant | 0.1 |
clpC1 | 4038315 | p.Gly797Val | missense_variant | 0.11 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243192 | c.-41A>C | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4245261 | p.Lys677Glu | missense_variant | 0.1 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
whiB6 | 4338563 | c.-42G>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |