| Variant ID: vg0815410001 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 15410001 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 218. )
GGCGGTAATAACCCGCAAGTCCTAAGAAACTCCGAACCTGAGTGACTGTCCTTGGTGGGGTCCATTTGGTAACTGACTCCACATTTGCTGGATCCACAGC[T/C]
ACTCCTTGAGCATTCACGATGTGACCAAGAAACTGAACTTCCTTAAGCCAGAAGTCGCACTTGCTGAACTTGGCATATAGCTGGTGCTCTTTTAACTTTT
AAAAGTTAAAAGAGCACCAGCTATATGCCAAGTTCAGCAAGTGCGACTTCTGGCTTAAGGAAGTTCAGTTTCTTGGTCACATCGTGAATGCTCAAGGAGT[A/G]
GCTGTGGATCCAGCAAATGTGGAGTCAGTTACCAAATGGACCCCACCAAGGACAGTCACTCAGGTTCGGAGTTTCTTAGGACTTGCGGGTTATTACCGCC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.70% | 0.30% | 12.00% | 67.01% | NA |
| All Indica | 2759 | 1.10% | 0.00% | 12.87% | 85.97% | NA |
| All Japonica | 1512 | 60.50% | 0.90% | 6.42% | 32.21% | NA |
| Aus | 269 | 2.20% | 0.00% | 34.94% | 62.83% | NA |
| Indica I | 595 | 0.50% | 0.20% | 1.18% | 98.15% | NA |
| Indica II | 465 | 1.90% | 0.00% | 8.39% | 89.68% | NA |
| Indica III | 913 | 0.50% | 0.00% | 21.69% | 77.77% | NA |
| Indica Intermediate | 786 | 1.80% | 0.00% | 14.12% | 84.10% | NA |
| Temperate Japonica | 767 | 83.70% | 0.00% | 2.22% | 14.08% | NA |
| Tropical Japonica | 504 | 28.80% | 2.40% | 9.52% | 59.33% | NA |
| Japonica Intermediate | 241 | 53.10% | 0.40% | 13.28% | 33.20% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 7.29% | 89.58% | NA |
| Intermediate | 90 | 25.60% | 0.00% | 15.56% | 58.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0815410001 | T -> C | LOC_Os08g25330.1 | synonymous_variant ; p.Val795Val; LOW | synonymous_codon | Average:4.486; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0815410001 | T -> DEL | LOC_Os08g25330.1 | N | frameshift_variant | Average:4.486; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |