| Variant ID: vg0815410091 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 15410091 |
| 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: 120. )
GATCCACAGCTACTCCTTGAGCATTCACGATGTGACCAAGAAACTGAACTTCCTTAAGCCAGAAGTCGCACTTGCTGAACTTGGCATATAGCTGGTGCTC[T/C]
TTTAACTTTTCAAGTACCAGCCGAAGATGCTGCTCATGTTCTTCCTCGGACTTGGAGTAGATAAGTATGTCATCGATGAAAACCATGACAAACTTGTCTA
TAGACAAGTTTGTCATGGTTTTCATCGATGACATACTTATCTACTCCAAGTCCGAGGAAGAACATGAGCAGCATCTTCGGCTGGTACTTGAAAAGTTAAA[A/G]
GAGCACCAGCTATATGCCAAGTTCAGCAAGTGCGACTTCTGGCTTAAGGAAGTTCAGTTTCTTGGTCACATCGTGAATGCTCAAGGAGTAGCTGTGGATC
| 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 | 19.90% | 0.00% | 11.24% | 68.81% | NA |
| All Indica | 2759 | 0.70% | 0.00% | 11.67% | 87.68% | NA |
| All Japonica | 1512 | 59.50% | 0.10% | 7.08% | 33.40% | NA |
| Aus | 269 | 0.40% | 0.00% | 34.57% | 65.06% | NA |
| Indica I | 595 | 0.00% | 0.00% | 0.34% | 99.66% | NA |
| Indica II | 465 | 1.10% | 0.00% | 7.96% | 90.97% | NA |
| Indica III | 913 | 0.20% | 0.00% | 20.04% | 79.74% | NA |
| Indica Intermediate | 786 | 1.40% | 0.00% | 12.72% | 85.88% | NA |
| Temperate Japonica | 767 | 84.00% | 0.00% | 2.74% | 13.30% | NA |
| Tropical Japonica | 504 | 27.40% | 0.20% | 9.13% | 63.29% | NA |
| Japonica Intermediate | 241 | 48.50% | 0.00% | 16.60% | 34.85% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 2.08% | 96.88% | NA |
| Intermediate | 90 | 25.60% | 0.00% | 7.78% | 66.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0815410091 | T -> C | LOC_Os08g25330.1 | synonymous_variant ; p.Lys765Lys; LOW | synonymous_codon | Average:4.467; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0815410091 | T -> DEL | LOC_Os08g25330.1 | N | frameshift_variant | Average:4.467; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |