Run ID: SRR25827644
Sample name:
Date: 02-02-2024 13:21:32
Number of reads: 8473547
Percentage reads mapped: 99.17
Strain: lineage2.2.1.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | fabG1 c.-15C>T (0.20), katG p.Ser315Thr (0.99) |
Ethambutol | R | embA c.-11C>A (0.23), embB p.Met306Val (1.00) |
Pyrazinamide | R | pncA p.Val139Ala (0.82), pncA p.Leu27Pro (0.23) |
Streptomycin | R | rpsL p.Lys43Arg (0.99) |
Fluoroquinolones | R | gyrA p.Ala90Val (0.22), gyrA p.Asp94Gly (0.76) |
Moxifloxacin | R | gyrA p.Ala90Val (0.22), gyrA p.Asp94Gly (0.76) |
Ofloxacin | R | gyrA p.Ala90Val (0.22), gyrA p.Asp94Gly (0.76) |
Levofloxacin | R | gyrA p.Ala90Val (0.22), gyrA p.Asp94Gly (0.76) |
Ciprofloxacin | R | gyrA p.Ala90Val (0.22), gyrA p.Asp94Gly (0.76) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | fabG1 c.-15C>T (0.20) |
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 |
lineage2.2.1.1 | East-Asian (Beijing) | Beijing-RD150 | RD105;RD207;RD181;RD150 | 0.78 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.22 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.76 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.99 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.2 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.99 | isoniazid |
pncA | 2288826 | p.Val139Ala | missense_variant | 0.82 | pyrazinamide |
pncA | 2289162 | p.Leu27Pro | missense_variant | 0.23 | pyrazinamide |
embA | 4243222 | c.-11C>A | upstream_gene_variant | 0.23 | ethambutol |
embB | 4247429 | p.Met306Val | 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 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.76 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764363 | p.Gly332Ser | missense_variant | 0.86 |
rpoC | 766488 | p.Pro1040Arg | missense_variant | 0.27 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.79 |
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 | 0.99 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.99 |
PPE35 | 2170306 | p.Ala103Thr | missense_variant | 0.21 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
eis | 2714846 | p.Val163Ile | missense_variant | 0.76 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
whiB7 | 3568435 | c.242_245delGTCCinsATCCTT | frameshift_variant&missense_variant | 0.26 |
whiB7 | 3568442 | p.Lys80Gln | missense_variant | 0.24 |
whiB7 | 3568443 | p.His79Gln | missense_variant | 0.24 |
whiB7 | 3568735 | c.-56G>T | upstream_gene_variant | 0.77 |
whiB7 | 3568854 | c.-176delG | upstream_gene_variant | 0.27 |
Rv3236c | 3612813 | p.Thr102Ala | missense_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 | 0.2 |
embB | 4247880 | p.Val456Ala | missense_variant | 0.75 |
embB | 4248115 | c.1602C>T | synonymous_variant | 0.73 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.99 |
ethA | 4326513 | p.Thr321Pro | missense_variant | 0.2 |
ethA | 4326676 | p.Ser266Arg | missense_variant | 0.24 |
whiB6 | 4338410 | p.Pro38Ala | missense_variant | 0.77 |
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 |