| Variant ID: vg1220960479 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960479 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 272. )
CTCACAAGGCATCTGAGGCGAGGAATTTGGCACCTCTAGAACTTGTTCATTCCGATTTGTGCGAAATGAACGGCGTGTTGACTAAAGGGGGAAAGAAATA[T/C]
TTCATGACACTGATAGATGATTGCACTAGATTTTGCTATGTGTATCTATTGAAAACAAAGGATGAGGCATTGCATTTCTTTAAAATCTATAAAGCTGAGG
CCTCAGCTTTATAGATTTTAAAGAAATGCAATGCCTCATCCTTTGTTTTCAATAGATACACATAGCAAAATCTAGTGCAATCATCTATCAGTGTCATGAA[A/G]
TATTTCTTTCCCCCTTTAGTCAACACGCCGTTCATTTCGCACAAATCGGAATGAACAAGTTCTAGAGGTGCCAAATTCCTCGCCTCAGATGCCTTGTGAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 57.80% | 0.40% | 1.18% | 40.61% | NA |
| All Indica | 2759 | 78.90% | 0.10% | 0.54% | 20.37% | NA |
| All Japonica | 1512 | 23.90% | 0.80% | 2.45% | 72.88% | NA |
| Aus | 269 | 51.70% | 0.40% | 0.74% | 47.21% | NA |
| Indica I | 595 | 62.50% | 0.00% | 1.01% | 36.47% | NA |
| Indica II | 465 | 79.10% | 0.00% | 0.22% | 20.65% | NA |
| Indica III | 913 | 88.60% | 0.20% | 0.22% | 10.95% | NA |
| Indica Intermediate | 786 | 80.00% | 0.30% | 0.76% | 18.96% | NA |
| Temperate Japonica | 767 | 10.40% | 0.00% | 0.26% | 89.31% | NA |
| Tropical Japonica | 504 | 40.30% | 2.20% | 5.95% | 51.59% | NA |
| Japonica Intermediate | 241 | 32.40% | 0.40% | 2.07% | 65.15% | NA |
| VI/Aromatic | 96 | 15.60% | 1.00% | 0.00% | 83.33% | NA |
| Intermediate | 90 | 44.40% | 0.00% | 2.22% | 53.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960479 | T -> C | LOC_Os12g34580.1 | synonymous_variant ; p.Tyr621Tyr; LOW | synonymous_codon | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1220960479 | T -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |