Run ID: SRR8651558
Sample name:
Date: 21-10-2023 12:59:23
Number of reads: 9597603
Percentage reads mapped: 99.48
Strain: lineage2.2.2
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Asp435Val (1.00) |
Isoniazid | R | katG p.Ser315Asn (0.99) |
Ethambutol | R | embB p.Met306Val (1.00) |
Pyrazinamide | R | pncA p.Met175Arg (0.99) |
Streptomycin | R | rrs n.514A>C (1.00) |
Fluoroquinolones | R | gyrA p.Ala90Val (1.00), gyrA p.Asp94Asn (1.00) |
Moxifloxacin | R | gyrA p.Ala90Val (1.00), gyrA p.Asp94Asn (1.00) |
Ofloxacin | R | gyrA p.Ala90Val (1.00), gyrA p.Asp94Asn (1.00) |
Levofloxacin | R | gyrA p.Ala90Val (1.00), gyrA p.Asp94Asn (1.00) |
Ciprofloxacin | R | gyrA p.Ala90Val (1.00), gyrA p.Asp94Asn (1.00) |
Aminoglycosides | R | rrs n.1401A>G (0.98) |
Amikacin | R | rrs n.1401A>G (0.98) |
Capreomycin | R | rrs n.1401A>G (0.98) |
Kanamycin | R | rrs n.1401A>G (0.98) |
Cycloserine | ||
Ethionamide | R | ethA c.1054delG (1.00), ethA c.1054delG (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 |
lineage2.2.2 | East-Asian (Beijing) | Beijing-RD105/RD207 | RD105;RD207 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7581 | p.Asp94Asn | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761110 | p.Asp435Val | missense_variant | 1.0 | rifampicin |
rrs | 1472359 | n.514A>C | non_coding_transcript_exon_variant | 1.0 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.98 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Asn | missense_variant | 0.99 | isoniazid |
pncA | 2288718 | p.Met175Arg | missense_variant | 0.99 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
ethA | 4326419 | c.1054delG | frameshift_variant | 1.0 | ethionamide, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6773 | p.Gly512Arg | missense_variant | 0.98 |
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 | 491284 | p.Gly168Arg | missense_variant | 0.99 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.99 |
rpoB | 760235 | c.429T>C | synonymous_variant | 0.99 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpR5 | 779101 | c.114_132delATTGTTGGGCTGGCTGCTG | frameshift_variant | 1.0 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_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 |
PPE35 | 2169044 | c.1569G>C | synonymous_variant | 0.14 |
PPE35 | 2169047 | p.Ile522Val | missense_variant | 0.16 |
PPE35 | 2169053 | c.1560T>C | synonymous_variant | 0.18 |
PPE35 | 2169056 | c.1557A>G | synonymous_variant | 0.19 |
PPE35 | 2169063 | p.Met517Thr | missense_variant | 0.21 |
PPE35 | 2169066 | p.Ala516Val | missense_variant | 0.23 |
PPE35 | 2169071 | c.1542A>G | synonymous_variant | 0.29 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
alr | 3841419 | p.Val1Gly | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.99 |
embB | 4248109 | c.1596C>A | synonymous_variant | 0.99 |
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 |