| Variant ID: vg1220960391 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960391 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 309. )
TTAGCTAACATGAGTTTAATTCCAAAATTCACTTTGGTAAAAGGTTCCAAGTGCCATACTTGTGTTCAATCGAAACAACCTCGCAAGCCTCACAAGGCAT[C/A]
TGAGGCGAGGAATTTGGCACCTCTAGAACTTGTTCATTCCGATTTGTGCGAAATGAACGGCGTGTTGACTAAAGGGGGAAAGAAATATTTCATGACACTG
CAGTGTCATGAAATATTTCTTTCCCCCTTTAGTCAACACGCCGTTCATTTCGCACAAATCGGAATGAACAAGTTCTAGAGGTGCCAAATTCCTCGCCTCA[G/T]
ATGCCTTGTGAGGCTTGCGAGGTTGTTTCGATTGAACACAAGTATGGCACTTGGAACCTTTTACCAAAGTGAATTTTGGAATTAAACTCATGTTAGCTAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 1.90% | 0.10% | 12.78% | 85.23% | NA |
| All Indica | 2759 | 2.90% | 0.20% | 13.34% | 83.54% | NA |
| All Japonica | 1512 | 0.30% | 0.00% | 9.85% | 89.88% | NA |
| Aus | 269 | 0.40% | 0.00% | 27.51% | 72.12% | NA |
| Indica I | 595 | 1.80% | 0.00% | 10.42% | 87.73% | NA |
| Indica II | 465 | 4.90% | 0.60% | 10.75% | 83.66% | NA |
| Indica III | 913 | 2.60% | 0.20% | 18.29% | 78.86% | NA |
| Indica Intermediate | 786 | 2.90% | 0.00% | 11.32% | 85.75% | NA |
| Temperate Japonica | 767 | 0.10% | 0.00% | 6.52% | 93.35% | NA |
| Tropical Japonica | 504 | 0.60% | 0.00% | 11.11% | 88.29% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 17.84% | 82.16% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 3.30% | 0.00% | 14.44% | 82.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960391 | C -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1220960391 | C -> A | LOC_Os12g34580.1 | missense_variant ; p.Ser592Tyr; MODERATE | nonsynonymous_codon ; S592Y | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.00 |