| Variant ID: vg1220962472 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20962472 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 300. )
TCCAAAAGTACTAGAAGGGTATAGTGACTCAAACTGGATATCTGATGCTGATGAGATAAAAGCCACAAGTGGATATGTGTTCACACTTGGAGGTGGCGCT[G/A]
TTTCCTGGAAGTCTTGCAAGCAGACCATCTTAACGAGGTCAACAATGGAAGCATAACTTACAGCACTAGATACTGCGACAGTTGAGGCCGAGTGGCTTCG
CGAAGCCACTCGGCCTCAACTGTCGCAGTATCTAGTGCTGTAAGTTATGCTTCCATTGTTGACCTCGTTAAGATGGTCTGCTTGCAAGACTTCCAGGAAA[C/T]
AGCGCCACCTCCAAGTGTGAACACATATCCACTTGTGGCTTTTATCTCATCAGCATCAGATATCCAGTTTGAGTCACTATACCCTTCTAGTACTTTTGGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.90% | 0.10% | 7.72% | 91.24% | NA |
| All Indica | 2759 | 0.50% | 0.10% | 3.37% | 95.94% | NA |
| All Japonica | 1512 | 1.90% | 0.10% | 17.33% | 80.75% | NA |
| Aus | 269 | 0.00% | 0.00% | 1.12% | 98.88% | NA |
| Indica I | 595 | 0.00% | 0.00% | 0.50% | 99.50% | NA |
| Indica II | 465 | 1.70% | 0.20% | 4.73% | 93.33% | NA |
| Indica III | 913 | 0.00% | 0.20% | 4.05% | 95.73% | NA |
| Indica Intermediate | 786 | 0.90% | 0.10% | 3.94% | 95.04% | NA |
| Temperate Japonica | 767 | 3.40% | 0.00% | 24.12% | 72.49% | NA |
| Tropical Japonica | 504 | 0.00% | 0.20% | 4.56% | 95.24% | NA |
| Japonica Intermediate | 241 | 0.80% | 0.00% | 22.41% | 76.76% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 7.78% | 91.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220962472 | G -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:7.776; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg1220962472 | G -> A | LOC_Os12g34580.1 | missense_variant ; p.Val1286Ile; MODERATE | nonsynonymous_codon ; V1286I | Average:7.776; most accessible tissue: Minghui63 root, score: 13.235 | unknown | unknown | TOLERATED | 0.05 |