| Variant ID: vg1220961206 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20961206 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 404. )
TGAGAATGAATTTCCTATGAAATATACACCTAGCACTTCTAGTAAAGAAACTGTCATGCCCCATGAGCACTTTGCACCGATAGAACACAATGATCAAACG[C/A]
CTGAGGAAAATCCTGAGGAGGACAACATTGTAGATACTCGCAAGAGTAAGAGACAAAGGGTTGCAAAATCCTTTGGAGATGACTACATTGTATACCTCGT
ACGAGGTATACAATGTAGTCATCTCCAAAGGATTTTGCAACCCTTTGTCTCTTACTCTTGCGAGTATCTACAATGTTGTCCTCCTCAGGATTTTCCTCAG[G/T]
CGTTTGATCATTGTGTTCTATCGGTGCAAAGTGCTCATGGGGCATGACAGTTTCTTTACTAGAAGTGCTAGGTGTATATTTCATAGGAAATTCATTCTCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 1.50% | 0.90% | 4.06% | 93.53% | NA |
| All Indica | 2759 | 1.60% | 1.20% | 3.62% | 93.58% | NA |
| All Japonica | 1512 | 1.30% | 0.40% | 5.22% | 93.06% | NA |
| Aus | 269 | 1.50% | 1.10% | 2.60% | 94.80% | NA |
| Indica I | 595 | 0.80% | 0.00% | 1.01% | 98.15% | NA |
| Indica II | 465 | 1.10% | 2.60% | 3.44% | 92.90% | NA |
| Indica III | 913 | 2.40% | 1.30% | 5.59% | 90.69% | NA |
| Indica Intermediate | 786 | 1.40% | 1.30% | 3.44% | 93.89% | NA |
| Temperate Japonica | 767 | 1.60% | 0.10% | 4.17% | 94.13% | NA |
| Tropical Japonica | 504 | 0.80% | 0.80% | 3.57% | 94.84% | 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 | 2.20% | 1.10% | 6.67% | 90.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220961206 | C -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1220961206 | C -> A | LOC_Os12g34580.1 | missense_variant ; p.Pro864Thr; MODERATE | nonsynonymous_codon ; P864T | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 0.43 |