Run ID: SRR21887760
Sample name:
Date: 07-07-2023 07:25:59
Number of reads: 11900552
Percentage reads mapped: 99.57
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Phe424Val (1.00), rpoB p.Leu430Pro (1.00) |
Isoniazid | R | katG p.Ser315Asn (1.00), ahpC c.-48G>A (1.00) |
Ethambutol | R | embB p.Met306Ile (0.99), embB p.Gln497Pro (1.00) |
Pyrazinamide | R | pncA c.393dupC (1.00), pncA c.393dupC (1.00) |
Streptomycin | R | rpsL p.Lys43Arg (0.98) |
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 | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
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 | 761076 | p.Phe424Val | missense_variant | 1.0 | rifampicin |
rpoB | 761095 | p.Leu430Pro | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.98 | streptomycin |
katG | 2155168 | p.Ser315Asn | missense_variant | 1.0 | isoniazid |
pncA | 2288848 | c.393dupC | frameshift_variant | 1.0 | pyrazinamide, pyrazinamide |
ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 1.0 | isoniazid |
embB | 4247431 | p.Met306Ile | missense_variant | 0.99 | ethambutol |
embB | 4248003 | p.Gln497Pro | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
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 |
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 | 779309 | c.321dupC | frameshift_variant | 1.0 |
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 |
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 |
katG | 2156264 | c.-153C>T | upstream_gene_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
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 |
fbiB | 3641970 | p.Val146Leu | missense_variant | 1.0 |
rpoA | 3878614 | c.-107A>C | upstream_gene_variant | 0.15 |
rpoA | 3878619 | c.-112A>C | upstream_gene_variant | 0.15 |
rpoA | 3878641 | c.-135delG | upstream_gene_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.16 |
embB | 4247033 | p.Ser174Arg | missense_variant | 0.15 |
embB | 4247039 | p.Phe176Val | missense_variant | 0.2 |
embB | 4247055 | p.Leu181Gln | missense_variant | 0.17 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
whiB6 | 4338440 | c.81_82insA | frameshift_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 |