| Variant ID: vg1220960512 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960512 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 128. )
CTCTAGAACTTGTTCATTCCGATTTGTGCGAAATGAACGGCGTGTTGACTAAAGGGGGAAAGAAATATTTCATGACACTGATAGATGATTGCACTAGATT[T/C]
TGCTATGTGTATCTATTGAAAACAAAGGATGAGGCATTGCATTTCTTTAAAATCTATAAAGCTGAGGTAGAAAACCAACTTGAAAGGAAAATTAAACGGT
ACCGTTTAATTTTCCTTTCAAGTTGGTTTTCTACCTCAGCTTTATAGATTTTAAAGAAATGCAATGCCTCATCCTTTGTTTTCAATAGATACACATAGCA[A/G]
AATCTAGTGCAATCATCTATCAGTGTCATGAAATATTTCTTTCCCCCTTTAGTCAACACGCCGTTCATTTCGCACAAATCGGAATGAACAAGTTCTAGAG
| 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 | 1.80% | 0.20% | 3.94% | 94.01% | NA |
| All Indica | 2759 | 0.50% | 0.30% | 3.33% | 95.90% | NA |
| All Japonica | 1512 | 4.80% | 0.10% | 5.29% | 89.88% | NA |
| Aus | 269 | 0.40% | 0.00% | 2.23% | 97.40% | NA |
| Indica I | 595 | 0.00% | 0.00% | 1.51% | 98.49% | NA |
| Indica II | 465 | 0.60% | 0.00% | 0.86% | 98.49% | NA |
| Indica III | 913 | 0.70% | 0.50% | 7.01% | 91.79% | NA |
| Indica Intermediate | 786 | 0.60% | 0.30% | 1.91% | 97.20% | NA |
| Temperate Japonica | 767 | 1.40% | 0.00% | 2.74% | 95.83% | NA |
| Tropical Japonica | 504 | 4.40% | 0.20% | 8.33% | 87.10% | NA |
| Japonica Intermediate | 241 | 16.20% | 0.00% | 7.05% | 76.76% | NA |
| VI/Aromatic | 96 | 0.00% | 1.00% | 0.00% | 98.96% | NA |
| Intermediate | 90 | 0.00% | 1.10% | 8.89% | 90.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960512 | T -> C | LOC_Os12g34580.1 | synonymous_variant ; p.Phe632Phe; LOW | synonymous_codon | Average:5.161; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |
| vg1220960512 | T -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:5.161; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |