| Variant ID: vg0410565119 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10565119 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATTCCTTATGGAAAAATCAAAAGGAAATTCCATCTTCTATTTCTTTCAAAGTGCACAGAAATTGCAAAGTAAGCAAAAGAGAACCAGGCTCATCTACCAC[A/G]
ACAAATCTCTGCCAACCAACAACTTTCCAAATAGCACGAAAATCAACATCCATACCTATCTTTTTCAGCAGCTCCGGAGAGTATTCTCGTGTGTGAGCAT
ATGCTCACACACGAGAATACTCTCCGGAGCTGCTGAAAAAGATAGGTATGGATGTTGATTTTCGTGCTATTTGGAAAGTTGTTGGTTGGCAGAGATTTGT[T/C]
GTGGTAGATGAGCCTGGTTCTCTTTTGCTTACTTTGCAATTTCTGTGCACTTTGAAAGAAATAGAAGATGGAATTTCCTTTTGATTTTTCCATAAGGAAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.60% | 1.10% | 2.86% | 56.45% | NA |
| All Indica | 2759 | 8.30% | 1.90% | 4.82% | 84.92% | NA |
| All Japonica | 1512 | 99.10% | 0.00% | 0.00% | 0.86% | NA |
| Aus | 269 | 1.10% | 0.00% | 0.00% | 98.88% | NA |
| Indica I | 595 | 5.50% | 2.20% | 7.23% | 85.04% | NA |
| Indica II | 465 | 24.90% | 0.90% | 4.30% | 69.89% | NA |
| Indica III | 913 | 2.30% | 2.40% | 3.50% | 91.79% | NA |
| Indica Intermediate | 786 | 7.60% | 1.80% | 4.83% | 85.75% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 0.00% | 13.54% | NA |
| Intermediate | 90 | 61.10% | 0.00% | 2.22% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410565119 | A -> DEL | LOC_Os04g19010.1 | N | frameshift_variant | Average:7.615; most accessible tissue: Callus, score: 15.368 | N | N | N | N |
| vg0410565119 | A -> G | LOC_Os04g19010.1 | synonymous_variant ; p.Val68Val; LOW | synonymous_codon | Average:7.615; most accessible tissue: Callus, score: 15.368 | N | N | N | N |