Run ID: SRR25827727
Sample name:
Date: 02-02-2024 16:50:12
Number of reads: 23420120
Percentage reads mapped: 97.16
Strain: lineage2.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.His445Leu (0.30), rpoB p.Ser450Leu (0.68) |
Isoniazid | R | fabG1 c.-15C>T (1.00), katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Met306Val (0.69), embB p.Gln497Arg (0.67) |
Pyrazinamide | R | pncA p.Gly132Ala (0.55), pncA p.Thr47Ala (0.44) |
Streptomycin | R | rpsL p.Lys43Arg (0.72) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | R | eis c.-37G>T (0.49) |
Cycloserine | ||
Ethionamide | R | fabG1 c.-15C>T (1.00) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid | R | rplC p.Cys154Arg (0.44) |
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 | 761140 | p.His445Leu | missense_variant | 0.3 | rifampicin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.68 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.72 | streptomycin |
rplC | 801268 | p.Cys154Arg | missense_variant | 0.44 | linezolid |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288847 | p.Gly132Ala | missense_variant | 0.55 | pyrazinamide |
pncA | 2289103 | p.Thr47Ala | missense_variant | 0.44 | pyrazinamide |
eis | 2715369 | c.-37G>T | upstream_gene_variant | 0.49 | kanamycin |
embB | 4247429 | p.Met306Val | missense_variant | 0.69 | ethambutol |
embB | 4248003 | p.Gln497Arg | missense_variant | 0.67 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7581 | p.Asp94Cys | missense_variant | 0.57 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.94 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763501 | p.Asp44Glu | missense_variant | 0.69 |
rpoC | 764840 | p.Ile491Val | missense_variant | 0.48 |
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 | 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 |
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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
Rv2752c | 3064700 | p.Ser498Pro | missense_variant | 0.52 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3449738 | p.His412Arg | missense_variant | 0.53 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
embC | 4241022 | p.Ala387Val | missense_variant | 0.76 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
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 | 4407620 | p.Tyr195His | missense_variant | 0.42 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |