| Variant ID: vg1220960785 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960785 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 263. )
ATGAGATGACGCCTCCCTATTCACCCCAATCAAATGGGGTGGCCGAAAGAAAGAACCGTACTCTAACTGAGATGGTGAATGCCATGTTAGACACTGCGGG[G/A]
CTTTCCAAGGAATGGTGGGGTGAGGCAGTTTTGACTGCTTGTCATGTCCTGAATAAAATTCCAATGAAGCATAAGGAAGTAACACCATTCGAGGAATGGG
CCCATTCCTCGAATGGTGTTACTTCCTTATGCTTCATTGGAATTTTATTCAGGACATGACAAGCAGTCAAAACTGCCTCACCCCACCATTCCTTGGAAAG[C/T]
CCCGCAGTGTCTAACATGGCATTCACCATCTCAGTTAGAGTACGGTTCTTTCTTTCGGCCACCCCATTTGATTGGGGTGAATAGGGAGGCGTCATCTCAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 37.70% | 0.10% | 11.40% | 50.74% | NA |
| All Indica | 2759 | 61.00% | 0.10% | 13.27% | 25.63% | NA |
| All Japonica | 1512 | 3.80% | 0.10% | 8.47% | 87.57% | NA |
| Aus | 269 | 5.90% | 0.00% | 11.90% | 82.16% | NA |
| Indica I | 595 | 40.80% | 0.00% | 17.65% | 41.51% | NA |
| Indica II | 465 | 66.20% | 0.40% | 9.68% | 23.66% | NA |
| Indica III | 913 | 70.40% | 0.00% | 12.05% | 17.52% | NA |
| Indica Intermediate | 786 | 62.20% | 0.10% | 13.49% | 24.17% | NA |
| Temperate Japonica | 767 | 2.10% | 0.30% | 1.56% | 96.09% | NA |
| Tropical Japonica | 504 | 6.90% | 0.00% | 15.67% | 77.38% | NA |
| Japonica Intermediate | 241 | 2.90% | 0.00% | 15.35% | 81.74% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 4.17% | 90.62% | NA |
| Intermediate | 90 | 24.40% | 0.00% | 10.00% | 65.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960785 | G -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg1220960785 | G -> A | LOC_Os12g34580.1 | synonymous_variant ; p.Gly723Gly; LOW | synonymous_codon | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |