| Variant ID: vg1220960861 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960861 |
| 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: 313. )
GAATGCCATGTTAGACACTGCGGGGCTTTCCAAGGAATGGTGGGGTGAGGCAGTTTTGACTGCTTGTCATGTCCTGAATAAAATTCCAATGAAGCATAAG[G/A]
AAGTAACACCATTCGAGGAATGGGAAAGGAAGAAATTAAATCTCTCATACCTACGAACATGGGGCTGTTTGGCCAAGGTAAATGTACCTATAGCCAAAAA
TTTTTGGCTATAGGTACATTTACCTTGGCCAAACAGCCCCATGTTCGTAGGTATGAGAGATTTAATTTCTTCCTTTCCCATTCCTCGAATGGTGTTACTT[C/T]
CTTATGCTTCATTGGAATTTTATTCAGGACATGACAAGCAGTCAAAACTGCCTCACCCCACCATTCCTTGGAAAGCCCCGCAGTGTCTAACATGGCATTC
| 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 | 22.20% | 13.80% | 21.77% | 42.30% | NA |
| All Indica | 2759 | 35.70% | 10.80% | 31.46% | 22.11% | NA |
| All Japonica | 1512 | 1.30% | 19.20% | 4.70% | 74.74% | NA |
| Aus | 269 | 10.80% | 15.60% | 23.05% | 50.56% | NA |
| Indica I | 595 | 24.70% | 6.40% | 24.03% | 44.87% | NA |
| Indica II | 465 | 37.20% | 11.80% | 30.32% | 20.65% | NA |
| Indica III | 913 | 40.30% | 14.90% | 36.91% | 7.89% | NA |
| Indica Intermediate | 786 | 37.70% | 8.70% | 31.42% | 22.26% | NA |
| Temperate Japonica | 767 | 1.20% | 6.30% | 2.09% | 90.48% | NA |
| Tropical Japonica | 504 | 1.60% | 35.10% | 9.72% | 53.57% | NA |
| Japonica Intermediate | 241 | 1.20% | 27.40% | 2.49% | 68.88% | NA |
| VI/Aromatic | 96 | 1.00% | 3.10% | 15.62% | 80.21% | NA |
| Intermediate | 90 | 14.40% | 20.00% | 14.44% | 51.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960861 | G -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg1220960861 | G -> A | LOC_Os12g34580.1 | missense_variant ; p.Glu749Lys; MODERATE | nonsynonymous_codon ; E749K | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | unknown | unknown | TOLERATED | 0.07 |