| Variant ID: vg0802668766 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 2668766 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 313. )
CACCTCTATCAGACCTCAACCGTTTGATTTTCCTTTCAAGTTGGTTTTCTACCTCAGCTTTATAGATTTTAAAGAAATGCAATGCCTCATCCTTTGTTTT[C/T]
AATAGATACACATAGCAAAATCTAGTGCAATCATCTATCAGTGTCATGAAATATTTCTTTCCCCCTTTAGTCAACACGCCGTTCATTTCGCACAAATCGG
CCGATTTGTGCGAAATGAACGGCGTGTTGACTAAAGGGGGAAAGAAATATTTCATGACACTGATAGATGATTGCACTAGATTTTGCTATGTGTATCTATT[G/A]
AAAACAAAGGATGAGGCATTGCATTTCTTTAAAATCTATAAAGCTGAGGTAGAAAACCAACTTGAAAGGAAAATCAAACGGTTGAGGTCTGATAGAGGTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.40% | 0.30% | 15.91% | 25.39% | NA |
| All Indica | 2759 | 61.60% | 0.00% | 6.67% | 31.71% | NA |
| All Japonica | 1512 | 61.20% | 0.80% | 33.47% | 4.50% | NA |
| Aus | 269 | 4.50% | 0.00% | 7.43% | 88.10% | NA |
| Indica I | 595 | 82.00% | 0.00% | 14.96% | 3.03% | NA |
| Indica II | 465 | 77.20% | 0.00% | 6.88% | 15.91% | NA |
| Indica III | 913 | 41.80% | 0.00% | 2.30% | 55.86% | NA |
| Indica Intermediate | 786 | 59.90% | 0.00% | 5.34% | 34.73% | NA |
| Temperate Japonica | 767 | 50.60% | 0.00% | 42.63% | 6.78% | NA |
| Tropical Japonica | 504 | 73.40% | 2.40% | 22.42% | 1.79% | NA |
| Japonica Intermediate | 241 | 69.70% | 0.00% | 27.39% | 2.90% | NA |
| VI/Aromatic | 96 | 65.60% | 0.00% | 27.08% | 7.29% | NA |
| Intermediate | 90 | 67.80% | 0.00% | 17.78% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0802668766 | C -> T | LOC_Os08g05150.1 | synonymous_variant ; p.Leu626Leu; LOW | synonymous_codon | Average:10.896; most accessible tissue: Minghui63 flag leaf, score: 14.81 | N | N | N | N |
| vg0802668766 | C -> DEL | LOC_Os08g05150.1 | N | frameshift_variant | Average:10.896; most accessible tissue: Minghui63 flag leaf, score: 14.81 | N | N | N | N |