| Variant ID: vg1220960491 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960491 |
| 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: 268. )
CTGAGGCGAGGAATTTGGCACCTCTAGAACTTGTTCATTCCGATTTGTGCGAAATGAACGGCGTGTTGACTAAAGGGGGAAAGAAATATTTCATGACACT[G/A]
ATAGATGATTGCACTAGATTTTGCTATGTGTATCTATTGAAAACAAAGGATGAGGCATTGCATTTCTTTAAAATCTATAAAGCTGAGGTAGAAAACCAAC
GTTGGTTTTCTACCTCAGCTTTATAGATTTTAAAGAAATGCAATGCCTCATCCTTTGTTTTCAATAGATACACATAGCAAAATCTAGTGCAATCATCTAT[C/T]
AGTGTCATGAAATATTTCTTTCCCCCTTTAGTCAACACGCCGTTCATTTCGCACAAATCGGAATGAACAAGTTCTAGAGGTGCCAAATTCCTCGCCTCAG
| 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 | 34.60% | 4.50% | 20.25% | 40.65% | NA |
| All Indica | 2759 | 54.90% | 2.60% | 22.07% | 20.41% | NA |
| All Japonica | 1512 | 2.40% | 8.60% | 13.03% | 75.93% | NA |
| Aus | 269 | 21.20% | 2.60% | 37.92% | 38.29% | NA |
| Indica I | 595 | 32.40% | 1.20% | 22.69% | 43.70% | NA |
| Indica II | 465 | 58.50% | 1.50% | 21.08% | 18.92% | NA |
| Indica III | 913 | 65.80% | 4.40% | 24.32% | 5.48% | NA |
| Indica Intermediate | 786 | 57.10% | 2.30% | 19.59% | 20.99% | NA |
| Temperate Japonica | 767 | 1.70% | 1.70% | 6.13% | 90.48% | NA |
| Tropical Japonica | 504 | 4.00% | 13.70% | 25.40% | 56.94% | NA |
| Japonica Intermediate | 241 | 1.70% | 19.90% | 9.13% | 69.29% | NA |
| VI/Aromatic | 96 | 7.30% | 1.00% | 25.00% | 66.67% | NA |
| Intermediate | 90 | 21.10% | 3.30% | 27.78% | 47.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960491 | G -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1220960491 | G -> A | LOC_Os12g34580.1 | synonymous_variant ; p.Leu625Leu; LOW | synonymous_codon | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |