| Variant ID: vg1220960878 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960878 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 340. )
CTGCGGGGCTTTCCAAGGAATGGTGGGGTGAGGCAGTTTTGACTGCTTGTCATGTCCTGAATAAAATTCCAATGAAGCATAAGGAAGTAACACCATTCGA[G/A]
GAATGGGAAAGGAAGAAATTAAATCTCTCATACCTACGAACATGGGGCTGTTTGGCCAAGGTAAATGTACCTATAGCCAAAAAGCGGAAACTTGGACCAA
TTGGTCCAAGTTTCCGCTTTTTGGCTATAGGTACATTTACCTTGGCCAAACAGCCCCATGTTCGTAGGTATGAGAGATTTAATTTCTTCCTTTCCCATTC[C/T]
TCGAATGGTGTTACTTCCTTATGCTTCATTGGAATTTTATTCAGGACATGACAAGCAGTCAAAACTGCCTCACCCCACCATTCCTTGGAAAGCCCCGCAG
| 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 | 22.90% | 0.50% | 20.86% | 55.73% | NA |
| All Indica | 2759 | 30.60% | 0.60% | 27.00% | 41.75% | NA |
| All Japonica | 1512 | 11.40% | 0.10% | 9.92% | 78.57% | NA |
| Aus | 269 | 16.70% | 0.70% | 27.14% | 55.39% | NA |
| Indica I | 595 | 28.60% | 0.00% | 20.67% | 50.76% | NA |
| Indica II | 465 | 24.30% | 1.50% | 27.96% | 46.24% | NA |
| Indica III | 913 | 37.60% | 0.80% | 30.23% | 31.43% | NA |
| Indica Intermediate | 786 | 27.90% | 0.40% | 27.48% | 44.27% | NA |
| Temperate Japonica | 767 | 1.30% | 0.00% | 7.43% | 91.26% | NA |
| Tropical Japonica | 504 | 22.00% | 0.20% | 14.09% | 63.69% | NA |
| Japonica Intermediate | 241 | 21.20% | 0.40% | 9.13% | 69.29% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 7.29% | 90.62% | NA |
| Intermediate | 90 | 22.20% | 1.10% | 12.22% | 64.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960878 | G -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg1220960878 | G -> A | LOC_Os12g34580.1 | synonymous_variant ; p.Glu754Glu; LOW | synonymous_codon | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |