| Variant ID: vg0202706439 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 2706439 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 300. )
CGACTTGTGTTATTTCCATTGGAAACGGGTCACTTGGTGTGCGCCACGTTTCTTCACTAGAAGCGTCTGGCTGCTTATTGCTACCGGAATTTTGAGGAGC[G/A]
TTACCTTCTTGAGGCGCTATTGGTGTGTTCGATGGAACCTTTTCGTTCGACATCTTCCAACTTGACGTAAAAAAATTTGACATAAGTCCCAATTTTACGT
ACGTAAAATTGGGACTTATGTCAAATTTTTTTACGTCAAGTTGGAAGATGTCGAACGAAAAGGTTCCATCGAACACACCAATAGCGCCTCAAGAAGGTAA[C/T]
GCTCCTCAAAATTCCGGTAGCAATAAGCAGCCAGACGCTTCTAGTGAAGAAACGTGGCGCACACCAAGTGACCCGTTTCCAATGGAAATAACACAAGTCG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.90% | 0.50% | 2.88% | 59.69% | NA |
| All Indica | 2759 | 11.00% | 0.50% | 2.90% | 85.57% | NA |
| All Japonica | 1512 | 87.00% | 0.10% | 0.60% | 12.30% | NA |
| Aus | 269 | 26.00% | 2.60% | 14.50% | 56.88% | NA |
| Indica I | 595 | 15.30% | 0.00% | 2.18% | 82.52% | NA |
| Indica II | 465 | 3.70% | 0.60% | 1.51% | 94.19% | NA |
| Indica III | 913 | 13.30% | 1.00% | 2.96% | 82.80% | NA |
| Indica Intermediate | 786 | 9.40% | 0.40% | 4.20% | 86.01% | NA |
| Temperate Japonica | 767 | 81.70% | 0.00% | 0.52% | 17.73% | NA |
| Tropical Japonica | 504 | 98.20% | 0.00% | 0.60% | 1.19% | NA |
| Japonica Intermediate | 241 | 80.50% | 0.40% | 0.83% | 18.26% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 3.12% | 91.67% | NA |
| Intermediate | 90 | 57.80% | 0.00% | 5.56% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0202706439 | G -> A | LOC_Os02g05570.1 | synonymous_variant ; p.Asn18Asn; LOW | synonymous_codon | Average:5.229; most accessible tissue: Minghui63 flower, score: 9.27 | N | N | N | N |
| vg0202706439 | G -> DEL | LOC_Os02g05570.1 | N | frameshift_variant | Average:5.229; most accessible tissue: Minghui63 flower, score: 9.27 | N | N | N | N |