| Variant ID: vg1220960515 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960515 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 128. )
TAGAACTTGTTCATTCCGATTTGTGCGAAATGAACGGCGTGTTGACTAAAGGGGGAAAGAAATATTTCATGACACTGATAGATGATTGCACTAGATTTTG[C/T]
TATGTGTATCTATTGAAAACAAAGGATGAGGCATTGCATTTCTTTAAAATCTATAAAGCTGAGGTAGAAAACCAACTTGAAAGGAAAATTAAACGGTTGA
TCAACCGTTTAATTTTCCTTTCAAGTTGGTTTTCTACCTCAGCTTTATAGATTTTAAAGAAATGCAATGCCTCATCCTTTGTTTTCAATAGATACACATA[G/A]
CAAAATCTAGTGCAATCATCTATCAGTGTCATGAAATATTTCTTTCCCCCTTTAGTCAACACGCCGTTCATTTCGCACAAATCGGAATGAACAAGTTCTA
| 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 | 0.60% | 0.30% | 1.93% | 97.19% | NA |
| All Indica | 2759 | 0.30% | 0.10% | 1.92% | 97.72% | NA |
| All Japonica | 1512 | 1.10% | 0.90% | 2.45% | 95.57% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.37% | 99.63% | NA |
| Indica I | 595 | 0.00% | 0.00% | 0.67% | 99.33% | NA |
| Indica II | 465 | 0.00% | 0.20% | 1.29% | 98.49% | NA |
| Indica III | 913 | 0.70% | 0.10% | 3.83% | 95.40% | NA |
| Indica Intermediate | 786 | 0.30% | 0.00% | 1.02% | 98.73% | NA |
| Temperate Japonica | 767 | 0.00% | 1.40% | 1.83% | 96.74% | NA |
| Tropical Japonica | 504 | 1.20% | 0.40% | 1.79% | 96.63% | NA |
| Japonica Intermediate | 241 | 4.60% | 0.00% | 5.81% | 89.63% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 0.00% | 98.96% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 0.00% | 98.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960515 | C -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:5.161; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |
| vg1220960515 | C -> T | LOC_Os12g34580.1 | synonymous_variant ; p.Cys633Cys; LOW | synonymous_codon | Average:5.161; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |