| Variant ID: vg1220961247 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20961247 |
| Reference Allele: C | Alternative Allele: A,T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 395. )
GTAAAGAAACTGTCATGCCCCATGAGCACTTTGCACCGATAGAACACAATGATCAAACGCCTGAGGAAAATCCTGAGGAGGACAACATTGTAGATACTCG[C/A,T]
AAGAGTAAGAGACAAAGGGTTGCAAAATCCTTTGGAGATGACTACATTGTATACCTCGTGGATGACACCCCAAGAACCATAGAAGAGGCATATTCATCTC
GAGATGAATATGCCTCTTCTATGGTTCTTGGGGTGTCATCCACGAGGTATACAATGTAGTCATCTCCAAAGGATTTTGCAACCCTTTGTCTCTTACTCTT[G/T,A]
CGAGTATCTACAATGTTGTCCTCCTCAGGATTTTCCTCAGGCGTTTGATCATTGTGTTCTATCGGTGCAAAGTGCTCATGGGGCATGACAGTTTCTTTAC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 1.00% | 0.70% | 2.96% | 95.22% | C: 0.17% |
| All Indica | 2759 | 1.30% | 1.10% | 1.27% | 96.27% | C: 0.11% |
| All Japonica | 1512 | 0.40% | 0.10% | 6.28% | 92.92% | C: 0.26% |
| Aus | 269 | 1.10% | 0.00% | 1.86% | 96.65% | C: 0.37% |
| Indica I | 595 | 0.00% | 0.20% | 0.00% | 99.50% | C: 0.34% |
| Indica II | 465 | 3.00% | 0.20% | 1.94% | 94.84% | NA |
| Indica III | 913 | 1.30% | 2.00% | 1.64% | 94.96% | C: 0.11% |
| Indica Intermediate | 786 | 1.30% | 1.10% | 1.40% | 96.18% | NA |
| Temperate Japonica | 767 | 0.10% | 0.30% | 6.26% | 93.22% | C: 0.13% |
| Tropical Japonica | 504 | 0.80% | 0.00% | 3.17% | 95.83% | C: 0.20% |
| Japonica Intermediate | 241 | 0.40% | 0.00% | 12.86% | 85.89% | C: 0.83% |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 1.10% | 1.10% | 5.56% | 92.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220961247 | C -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1220961247 | C -> A | LOC_Os12g34580.1 | synonymous_variant ; p.Arg877Arg; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1220961247 | C -> T | LOC_Os12g34580.1 | synonymous_variant ; p.Arg877Arg; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |