| Variant ID: vg0224434814 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 24434814 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.70, G: 0.29, others allele: 0.00, population size: 78. )
CCAACTCGAACTTAATAAATAATCATGGGCAGGTTAGACATAGAGATTTGAGTGATTGTTATGCACGAATCCAACCGTACAGTAGCAGAATGAAGAAAGT[G/A]
GGAGCCTCTCAAGCGTGTGCGTACCGGGATCGCCGTCGCCGAAGCGCCGCTCTCCCGTCGTGAGCAGTCGGAGAGAATATTGTTGTTCCGGAGACGGAGG
CCTCCGTCTCCGGAACAACAATATTCTCTCCGACTGCTCACGACGGGAGAGCGGCGCTTCGGCGACGGCGATCCCGGTACGCACACGCTTGAGAGGCTCC[C/T]
ACTTTCTTCATTCTGCTACTGTACGGTTGGATTCGTGCATAACAATCACTCAAATCTCTATGTCTAACCTGCCCATGATTATTTATTAAGTTCGAGTTGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.40% | 24.70% | 0.40% | 19.55% | NA |
| All Indica | 2759 | 58.10% | 25.60% | 0.29% | 16.06% | NA |
| All Japonica | 1512 | 48.20% | 22.90% | 0.60% | 28.31% | NA |
| Aus | 269 | 71.70% | 16.70% | 0.00% | 11.52% | NA |
| Indica I | 595 | 45.70% | 18.50% | 0.34% | 35.46% | NA |
| Indica II | 465 | 76.30% | 19.60% | 0.22% | 3.87% | NA |
| Indica III | 913 | 52.20% | 32.20% | 0.11% | 15.44% | NA |
| Indica Intermediate | 786 | 63.40% | 26.80% | 0.51% | 9.29% | NA |
| Temperate Japonica | 767 | 39.90% | 23.20% | 0.78% | 36.11% | NA |
| Tropical Japonica | 504 | 63.30% | 24.80% | 0.40% | 11.51% | NA |
| Japonica Intermediate | 241 | 43.20% | 17.80% | 0.41% | 38.59% | NA |
| VI/Aromatic | 96 | 41.70% | 51.00% | 2.08% | 5.21% | NA |
| Intermediate | 90 | 57.80% | 23.30% | 0.00% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0224434814 | G -> A | LOC_Os02g40350.1 | downstream_gene_variant ; 1125.0bp to feature; MODIFIER | silent_mutation | Average:67.181; most accessible tissue: Zhenshan97 flower, score: 83.812 | N | N | N | N |
| vg0224434814 | G -> A | LOC_Os02g40340.1 | intron_variant ; MODIFIER | silent_mutation | Average:67.181; most accessible tissue: Zhenshan97 flower, score: 83.812 | N | N | N | N |
| vg0224434814 | G -> A | LOC_Os02g40340.2 | intron_variant ; MODIFIER | silent_mutation | Average:67.181; most accessible tissue: Zhenshan97 flower, score: 83.812 | N | N | N | N |
| vg0224434814 | G -> DEL | N | N | silent_mutation | Average:67.181; most accessible tissue: Zhenshan97 flower, score: 83.812 | N | N | N | N |