| Variant ID: vg0815411375 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 15411375 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 227. )
ACTTTCCAACCGTGTGTCCGGGTTTGTTACAATTGAAGCAGAGTTCGGGTTTTTCTCCCAACCTCTTGGGCTGTTCTGGCAGAGCTGGCTGAACTGATTG[A/C]
GCTGGAATCTTTAGTGAACTCGGAGTAGGGTTGAGGCTGTGCTGCTCACTATTGTTGTGACTGTCACTATGGTGGTTCTTGTTGAAGTTACCCGGGTGGT
ACCACCCGGGTAACTTCAACAAGAACCACCATAGTGACAGTCACAACAATAGTGAGCAGCACAGCCTCAACCCTACTCCGAGTTCACTAAAGATTCCAGC[T/G]
CAATCAGTTCAGCCAGCTCTGCCAGAACAGCCCAAGAGGTTGGGAGAAAAACCCGAACTCTGCTTCAATTGTAACAAACCCGGACACACGGTTGGAAAGT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 30.40% | 3.20% | 24.46% | 41.94% | NA |
| All Indica | 2759 | 3.20% | 3.50% | 23.67% | 69.59% | NA |
| All Japonica | 1512 | 74.00% | 3.00% | 21.56% | 1.39% | NA |
| Aus | 269 | 72.10% | 0.00% | 16.73% | 11.15% | NA |
| Indica I | 595 | 0.20% | 0.20% | 16.97% | 82.69% | NA |
| Indica II | 465 | 2.80% | 12.70% | 24.09% | 60.43% | NA |
| Indica III | 913 | 3.00% | 0.00% | 26.73% | 70.32% | NA |
| Indica Intermediate | 786 | 6.10% | 4.70% | 24.94% | 64.25% | NA |
| Temperate Japonica | 767 | 88.10% | 0.40% | 9.65% | 1.83% | NA |
| Tropical Japonica | 504 | 49.60% | 7.30% | 42.06% | 0.99% | NA |
| Japonica Intermediate | 241 | 80.10% | 2.50% | 16.60% | 0.83% | NA |
| VI/Aromatic | 96 | 7.30% | 1.00% | 90.62% | 1.04% | NA |
| Intermediate | 90 | 32.20% | 6.70% | 50.00% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0815411375 | A -> C | LOC_Os08g25330.1 | synonymous_variant ; p.Ala337Ala; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0815411375 | A -> DEL | LOC_Os08g25330.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |