| Variant ID: vg1220960810 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960810 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 123. )
CCAATCAAATGGGGTGGCCGAAAGAAAGAACCGTACTCTAACTGAGATGGTGAATGCCATGTTAGACACTGCGGGGCTTTCCAAGGAATGGTGGGGTGAG[G/A]
CAGTTTTGACTGCTTGTCATGTCCTGAATAAAATTCCAATGAAGCATAAGGAAGTAACACCATTCGAGGAATGGGAAAGGAAGAAATTAAATCTCTCATA
TATGAGAGATTTAATTTCTTCCTTTCCCATTCCTCGAATGGTGTTACTTCCTTATGCTTCATTGGAATTTTATTCAGGACATGACAAGCAGTCAAAACTG[C/T]
CTCACCCCACCATTCCTTGGAAAGCCCCGCAGTGTCTAACATGGCATTCACCATCTCAGTTAGAGTACGGTTCTTTCTTTCGGCCACCCCATTTGATTGG
| 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 | 32.00% | 13.50% | 14.98% | 39.46% | NA |
| All Indica | 2759 | 51.90% | 9.60% | 19.72% | 18.74% | NA |
| All Japonica | 1512 | 2.00% | 20.90% | 4.23% | 72.88% | NA |
| Aus | 269 | 11.50% | 13.80% | 24.91% | 49.81% | NA |
| Indica I | 595 | 33.30% | 5.90% | 20.67% | 40.17% | NA |
| Indica II | 465 | 61.50% | 8.40% | 12.69% | 17.42% | NA |
| Indica III | 913 | 57.70% | 13.10% | 23.55% | 5.59% | NA |
| Indica Intermediate | 786 | 53.60% | 9.20% | 18.70% | 18.58% | NA |
| Temperate Japonica | 767 | 2.00% | 6.50% | 2.09% | 89.44% | NA |
| Tropical Japonica | 504 | 2.20% | 39.30% | 7.94% | 50.60% | NA |
| Japonica Intermediate | 241 | 1.70% | 28.20% | 3.32% | 66.80% | NA |
| VI/Aromatic | 96 | 4.20% | 4.20% | 21.88% | 69.79% | NA |
| Intermediate | 90 | 17.80% | 18.90% | 13.33% | 50.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960810 | G -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg1220960810 | G -> A | LOC_Os12g34580.1 | missense_variant ; p.Ala732Thr; MODERATE | nonsynonymous_codon ; A732T | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | unknown | unknown | DELETERIOUS | 0.01 |