Run ID: ERR8025421
Sample name:
Date: 19-05-2023 15:27:13
Number of reads: 2660946
Percentage reads mapped: 99.6
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | fabG1 c.-15C>T (1.00), inhA p.Ile194Thr (1.00) |
Ethambutol | R | embB p.Met306Val (1.00) |
Pyrazinamide | ||
Streptomycin | ||
Fluoroquinolones | R | gyrA p.Asp94Ala (1.00) |
Moxifloxacin | R | gyrA p.Asp94Ala (1.00) |
Ofloxacin | R | gyrA p.Asp94Ala (1.00) |
Levofloxacin | R | gyrA p.Asp94Ala (1.00) |
Ciprofloxacin | R | gyrA p.Asp94Ala (1.00) |
Aminoglycosides | R | rrs n.1401A>G (1.00) |
Amikacin | R | rrs n.1401A>G (1.00) |
Capreomycin | R | rrs n.1401A>G (1.00) |
Kanamycin | R | rrs n.1401A>G (1.00) |
Cycloserine | ||
Ethionamide | R | fabG1 c.-15C>T (1.00), inhA p.Ile194Thr (1.00), ethR p.Ala95Thr (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 |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Ala | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
inhA | 1674782 | p.Ile194Thr | missense_variant | 1.0 | isoniazid, ethionamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
ethR | 4327831 | p.Ala95Thr | missense_variant | 1.0 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7774 | p.Gly158Val | missense_variant | 0.11 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575689 | c.342G>T | synonymous_variant | 0.12 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
mshA | 576574 | c.1227T>C | synonymous_variant | 0.11 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoB | 762286 | p.Arg827His | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763555 | c.186C>T | synonymous_variant | 1.0 |
rpoC | 764368 | c.999C>T | synonymous_variant | 0.11 |
rpoC | 767052 | p.Glu1228Gly | missense_variant | 0.2 |
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 | 778979 | c.-74G>T | upstream_gene_variant | 1.0 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781428 | c.-132C>T | upstream_gene_variant | 0.12 |
fbiC | 1304410 | p.Asp494Asn | missense_variant | 0.12 |
Rv1258c | 1406203 | p.Phe380Val | missense_variant | 0.1 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
fabG1 | 1673512 | c.78dupG | frameshift_variant | 0.12 |
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 |
pncA | 2290124 | c.-883C>A | upstream_gene_variant | 0.11 |
folC | 2747167 | p.Lys144Asn | missense_variant | 0.12 |
Rv2752c | 3065160 | p.Asn344Lys | missense_variant | 0.11 |
Rv2752c | 3065213 | p.Thr327Ala | missense_variant | 0.1 |
thyX | 3067483 | p.Ala155Thr | missense_variant | 0.12 |
thyX | 3067563 | p.Leu128Pro | missense_variant | 0.12 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339060 | c.-58C>T | upstream_gene_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
Rv3236c | 3613213 | c.-97C>T | upstream_gene_variant | 0.12 |
fbiA | 3640522 | c.-21_-20insG | upstream_gene_variant | 0.1 |
ddn | 3987110 | c.267C>T | synonymous_variant | 0.1 |
embA | 4242472 | c.-761G>A | upstream_gene_variant | 0.11 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242833 | p.Phe991Leu | missense_variant | 0.14 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4248250 | c.1737C>T | synonymous_variant | 0.15 |
aftB | 4267647 | p.Asp397Gly | missense_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 |