| Variant ID: vg1220961229 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20961229 |
| 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: 404. )
ATACACCTAGCACTTCTAGTAAAGAAACTGTCATGCCCCATGAGCACTTTGCACCGATAGAACACAATGATCAAACGCCTGAGGAAAATCCTGAGGAGGA[C/T]
AACATTGTAGATACTCGCAAGAGTAAGAGACAAAGGGTTGCAAAATCCTTTGGAGATGACTACATTGTATACCTCGTGGATGACACCCCAAGAACCATAG
CTATGGTTCTTGGGGTGTCATCCACGAGGTATACAATGTAGTCATCTCCAAAGGATTTTGCAACCCTTTGTCTCTTACTCTTGCGAGTATCTACAATGTT[G/A]
TCCTCCTCAGGATTTTCCTCAGGCGTTTGATCATTGTGTTCTATCGGTGCAAAGTGCTCATGGGGCATGACAGTTTCTTTACTAGAAGTGCTAGGTGTAT
| 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 | 2.90% | 1.00% | 5.92% | 90.25% | NA |
| All Indica | 2759 | 3.60% | 1.30% | 6.20% | 88.87% | NA |
| All Japonica | 1512 | 1.80% | 0.40% | 6.02% | 91.80% | NA |
| Aus | 269 | 0.70% | 1.10% | 3.72% | 94.42% | NA |
| Indica I | 595 | 0.70% | 0.00% | 2.02% | 97.31% | NA |
| Indica II | 465 | 1.30% | 3.00% | 6.45% | 89.25% | NA |
| Indica III | 913 | 6.90% | 1.30% | 10.19% | 81.60% | NA |
| Indica Intermediate | 786 | 3.40% | 1.30% | 4.58% | 90.71% | NA |
| Temperate Japonica | 767 | 2.20% | 0.10% | 4.82% | 92.83% | NA |
| Tropical Japonica | 504 | 1.20% | 0.80% | 4.96% | 93.06% | NA |
| Japonica Intermediate | 241 | 1.70% | 0.40% | 12.03% | 85.89% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 0.00% | 98.96% | NA |
| Intermediate | 90 | 5.60% | 1.10% | 8.89% | 84.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220961229 | C -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1220961229 | C -> T | LOC_Os12g34580.1 | synonymous_variant ; p.Asp871Asp; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |