| Variant ID: vg1117777843 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17777843 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 127. )
TTGTGCGGGATAACGTGCCTGTCAGTACGGTGTACTGGCGAAGAACAAGGGCACGTGGAGATCATGAGAGATTTGTCCCAGATTCGGAGAAAGAGATGCT[G/A]
TGGACCACAATGCTCGAGACATTCACCCTTCCTGCGGGTACAGAGGACAAAGTGAAAAGGTGGACTCTGAAGAAAATGGCAGAACAGTTTCAGAGCTTCA
TGAAGCTCTGAAACTGTTCTGCCATTTTCTTCAGAGTCCACCTTTTCACTTTGTCCTCTGTACCCGCAGGAAGGGTGAATGTCTCGAGCATTGTGGTCCA[C/T]
AGCATCTCTTTCTCCGAATCTGGGACAAATCTCTCATGATCTCCACGTGCCCTTGTTCTTCGCCAGTACACCGTACTGACAGGCACGTTATCCCGCACAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 1.00% | 0.30% | 5.25% | 93.42% | NA |
| All Indica | 2759 | 0.10% | 0.60% | 4.64% | 94.64% | NA |
| All Japonica | 1512 | 2.20% | 0.00% | 6.22% | 91.53% | NA |
| Aus | 269 | 0.70% | 0.00% | 1.49% | 97.77% | NA |
| Indica I | 595 | 0.30% | 0.30% | 2.35% | 96.97% | NA |
| Indica II | 465 | 0.20% | 0.60% | 12.04% | 87.10% | NA |
| Indica III | 913 | 0.10% | 0.70% | 2.85% | 96.39% | NA |
| Indica Intermediate | 786 | 0.00% | 0.60% | 4.07% | 95.29% | NA |
| Temperate Japonica | 767 | 2.20% | 0.00% | 9.52% | 88.27% | NA |
| Tropical Japonica | 504 | 2.20% | 0.00% | 0.60% | 97.22% | NA |
| Japonica Intermediate | 241 | 2.50% | 0.00% | 7.47% | 90.04% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 15.62% | 79.17% | NA |
| Intermediate | 90 | 2.20% | 0.00% | 7.78% | 90.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117777843 | G -> A | LOC_Os11g30552.1 | synonymous_variant ; p.Leu265Leu; LOW | synonymous_codon | Average:8.298; most accessible tissue: Minghui63 root, score: 15.664 | N | N | N | N |
| vg1117777843 | G -> DEL | LOC_Os11g30552.1 | N | frameshift_variant | Average:8.298; most accessible tissue: Minghui63 root, score: 15.664 | N | N | N | N |