| Variant ID: vg1220960437 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960437 |
| 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: 309. )
CCAAGTGCCATACTTGTGTTCAATCGAAACAACCTCGCAAGCCTCACAAGGCATCTGAGGCGAGGAATTTGGCACCTCTAGAACTTGTTCATTCCGATTT[G/A]
TGCGAAATGAACGGCGTGTTGACTAAAGGGGGAAAGAAATATTTCATGACACTGATAGATGATTGCACTAGATTTTGCTATGTGTATCTATTGAAAACAA
TTGTTTTCAATAGATACACATAGCAAAATCTAGTGCAATCATCTATCAGTGTCATGAAATATTTCTTTCCCCCTTTAGTCAACACGCCGTTCATTTCGCA[C/T]
AAATCGGAATGAACAAGTTCTAGAGGTGCCAAATTCCTCGCCTCAGATGCCTTGTGAGGCTTGCGAGGTTGTTTCGATTGAACACAAGTATGGCACTTGG
| 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 | 58.30% | 0.30% | 0.91% | 40.50% | NA |
| All Indica | 2759 | 78.90% | 0.10% | 0.62% | 20.37% | NA |
| All Japonica | 1512 | 25.10% | 0.70% | 1.59% | 72.55% | NA |
| Aus | 269 | 51.70% | 0.40% | 0.74% | 47.21% | NA |
| Indica I | 595 | 62.50% | 0.20% | 1.34% | 35.97% | NA |
| Indica II | 465 | 78.30% | 0.40% | 0.65% | 20.65% | NA |
| Indica III | 913 | 88.60% | 0.00% | 0.33% | 11.06% | NA |
| Indica Intermediate | 786 | 80.30% | 0.10% | 0.38% | 19.21% | NA |
| Temperate Japonica | 767 | 10.40% | 0.00% | 0.26% | 89.31% | NA |
| Tropical Japonica | 504 | 43.70% | 2.00% | 3.57% | 50.79% | NA |
| Japonica Intermediate | 241 | 33.20% | 0.40% | 1.66% | 64.73% | NA |
| VI/Aromatic | 96 | 16.70% | 0.00% | 0.00% | 83.33% | NA |
| Intermediate | 90 | 46.70% | 0.00% | 0.00% | 53.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960437 | G -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1220960437 | G -> A | LOC_Os12g34580.1 | synonymous_variant ; p.Leu607Leu; LOW | synonymous_codon | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |