| Variant ID: vg0435226116 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 35226116 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 117. )
CTGGCGCGCCAGGTAGGGGGCTCTGCGAGTGATCTTCTGAGCTCTCGCACTCTTTCGTGTGCGCCAAGCTTTTCCTGTTCAGCCCAATGGCCGAACAAGC[A/G]
AAGGCGCACAACCTCTCTCCGAGTGTTAGCGGTGACGACGGGGAGCCAAACCCACGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAAAGTCCTA
TAGGACTTTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCGTGGGTTTGGCTCCCCGTCGTCACCGCTAACACTCGGAGAGAGGTTGTGCGCCTT[T/C]
GCTTGTTCGGCCATTGGGCTGAACAGGAAAAGCTTGGCGCACACGAAAGAGTGCGAGAGCTCAGAAGATCACTCGCAGAGCCCCCTACCTGGCGCGCCAG
| 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 | 47.10% | 14.30% | 10.98% | 27.53% | NA |
| All Indica | 2759 | 11.70% | 24.50% | 18.30% | 45.45% | NA |
| All Japonica | 1512 | 99.30% | 0.10% | 0.13% | 0.53% | NA |
| Aus | 269 | 91.40% | 0.00% | 1.12% | 7.43% | NA |
| Indica I | 595 | 6.70% | 13.30% | 21.18% | 58.82% | NA |
| Indica II | 465 | 6.90% | 19.60% | 23.23% | 50.32% | NA |
| Indica III | 913 | 12.00% | 35.40% | 15.22% | 37.35% | NA |
| Indica Intermediate | 786 | 18.10% | 23.30% | 16.79% | 41.86% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 98.20% | 0.20% | 0.40% | 1.19% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 3.12% | 9.38% | NA |
| Intermediate | 90 | 81.10% | 1.10% | 6.67% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0435226116 | A -> DEL | LOC_Os04g59220.1 | N | frameshift_variant | Average:7.402; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |
| vg0435226116 | A -> G | LOC_Os04g59220.1 | synonymous_variant ; p.Ala5Ala; LOW | synonymous_codon | Average:7.402; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |