Variant ID: vg0118775740 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 18775740 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCTTCACTAAAATTAGACCATAACTCCTTTAGTAAAACCCTTTGATCAGCATGTTAAACATAATGCACTCTACCACTATATGAAATTACTTAATCTAATT[C/T]
AAAATATAACCACATGAAATGACATATATATAAGTTAAATAGTACATAGAGATGCAATTTTTTATTTTTATTTCATTTTTTTTGATATTTTTTTCGCACT
AGTGCGAAAAAAATATCAAAAAAAATGAAATAAAAATAAAAAATTGCATCTCTATGTACTATTTAACTTATATATATGTCATTTCATGTGGTTATATTTT[G/A]
AATTAGATTAAGTAATTTCATATAGTGGTAGAGTGCATTATGTTTAACATGCTGATCAAAGGGTTTTACTAAAGGAGTTATGGTCTAATTTTAGTGAAGG
Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 77.30% | 0.20% | 8.51% | 14.03% | NA |
All Indica | 2759 | 62.20% | 0.30% | 14.17% | 23.27% | NA |
All Japonica | 1512 | 99.10% | 0.00% | 0.20% | 0.73% | NA |
Aus | 269 | 97.00% | 0.40% | 1.12% | 1.49% | NA |
Indica I | 595 | 64.40% | 0.00% | 5.71% | 29.92% | NA |
Indica II | 465 | 45.40% | 0.20% | 29.46% | 24.95% | NA |
Indica III | 913 | 71.90% | 0.30% | 10.41% | 17.42% | NA |
Indica Intermediate | 786 | 59.40% | 0.60% | 15.90% | 24.05% | NA |
Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
Tropical Japonica | 504 | 97.80% | 0.00% | 0.60% | 1.59% | NA |
Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 87.80% | 0.00% | 5.56% | 6.67% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0118775740 | C -> T | LOC_Os01g34100.1 | upstream_gene_variant ; 4860.0bp to feature; MODIFIER | silent_mutation | Average:20.077; most accessible tissue: Zhenshan97 flag leaf, score: 28.494 | N | N | N | N |
vg0118775740 | C -> T | LOC_Os01g34080.1 | downstream_gene_variant ; 1264.0bp to feature; MODIFIER | silent_mutation | Average:20.077; most accessible tissue: Zhenshan97 flag leaf, score: 28.494 | N | N | N | N |
vg0118775740 | C -> T | LOC_Os01g34090.1 | downstream_gene_variant ; 2112.0bp to feature; MODIFIER | silent_mutation | Average:20.077; most accessible tissue: Zhenshan97 flag leaf, score: 28.494 | N | N | N | N |
vg0118775740 | C -> T | LOC_Os01g34080-LOC_Os01g34090 | intergenic_region ; MODIFIER | silent_mutation | Average:20.077; most accessible tissue: Zhenshan97 flag leaf, score: 28.494 | N | N | N | N |
vg0118775740 | C -> DEL | N | N | silent_mutation | Average:20.077; most accessible tissue: Zhenshan97 flag leaf, score: 28.494 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0118775740 | 2.19E-06 | NA | mr1734_2 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0118775740 | 6.60E-06 | 6.58E-06 | mr1755_2 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0118775740 | 4.08E-07 | NA | mr1782_2 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0118775740 | 3.27E-06 | NA | mr1893_2 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |