| Variant ID: vg0826581428 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 26581428 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 36. )
GGGTCACTCTGTGGCTGACAGCTATGAAATGCTTCTGGGTGAGTACTGGCAAACCTGAAGGAGTTCTTACTGCTGAACAACAGAAGCAATTCGAGGAAGC[T/C]
ACTACTCTCTTTGTGGGATGCATTCTTAGCGTTCTTGGCGATTGTCTGGTCGAGGTGTATATGCATATGACCGACGCTAAGGAGTTGTGGGATGCACTGA
TCAGTGCATCCCACAACTCCTTAGCGTCGGTCATATGCATATACACCTCGACCAGACAATCGCCAAGAACGCTAAGAATGCATCCCACAAAGAGAGTAGT[A/G]
GCTTCCTCGAATTGCTTCTGTTGTTCAGCAGTAAGAACTCCTTCAGGTTTGCCAGTACTCACCCAGAAGCATTTCATAGCTGTCAGCCACAGAGTGACCC
| 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 | 16.60% | 0.50% | 34.11% | 48.75% | NA |
| All Indica | 2759 | 0.70% | 0.00% | 38.38% | 60.89% | NA |
| All Japonica | 1512 | 48.60% | 1.30% | 25.86% | 24.27% | NA |
| Aus | 269 | 0.40% | 0.00% | 24.16% | 75.46% | NA |
| Indica I | 595 | 0.00% | 0.00% | 25.55% | 74.45% | NA |
| Indica II | 465 | 0.40% | 0.00% | 29.68% | 69.89% | NA |
| Indica III | 913 | 0.30% | 0.00% | 54.98% | 44.69% | NA |
| Indica Intermediate | 786 | 1.80% | 0.10% | 33.97% | 64.12% | NA |
| Temperate Japonica | 767 | 81.70% | 1.00% | 11.21% | 6.00% | NA |
| Tropical Japonica | 504 | 7.90% | 2.20% | 47.02% | 42.86% | NA |
| Japonica Intermediate | 241 | 28.20% | 0.00% | 28.22% | 43.57% | NA |
| VI/Aromatic | 96 | 10.40% | 4.20% | 67.71% | 17.71% | NA |
| Intermediate | 90 | 22.20% | 1.10% | 35.56% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0826581428 | T -> C | LOC_Os08g42090.1 | synonymous_variant ; p.Ala57Ala; LOW | synonymous_codon | Average:6.55; most accessible tissue: Zhenshan97 flower, score: 11.396 | N | N | N | N |
| vg0826581428 | T -> DEL | LOC_Os08g42090.1 | N | frameshift_variant | Average:6.55; most accessible tissue: Zhenshan97 flower, score: 11.396 | N | N | N | N |