| Variant ID: vg1101692555 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1692555 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 300. )
CGGCGCTCCTCCGCGCCATCGTCGGGATCGTGCACACCTGCCACTCCATGGGGGTGATCCACCGGGACCTCAAGCCGGAGAACTTCCTGCTGCTGAGCAA[G/A]
GGGGACGACGCGCCGCTCAAGGCCACCGACTTCGGCCTCTCCGTCTTCTTCAAGGAAGGCGAGGTGTTCCGCGACATCGTCGGCAGCGCCTACTACATCG
CGATGTAGTAGGCGCTGCCGACGATGTCGCGGAACACCTCGCCTTCCTTGAAGAAGACGGAGAGGCCGAAGTCGGTGGCCTTGAGCGGCGCGTCGTCCCC[C/T]
TTGCTCAGCAGCAGGAAGTTCTCCGGCTTGAGGTCCCGGTGGATCACCCCCATGGAGTGGCAGGTGTGCACGATCCCGACGATGGCGCGGAGGAGCGCCG
| 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 | 67.20% | 0.30% | 6.39% | 26.07% | NA |
| All Indica | 2759 | 48.00% | 0.50% | 10.08% | 41.50% | NA |
| All Japonica | 1512 | 98.50% | 0.00% | 0.07% | 1.46% | NA |
| Aus | 269 | 70.60% | 0.40% | 6.69% | 22.30% | NA |
| Indica I | 595 | 54.50% | 1.20% | 8.74% | 35.63% | NA |
| Indica II | 465 | 52.70% | 0.40% | 10.32% | 36.56% | NA |
| Indica III | 913 | 38.90% | 0.10% | 9.86% | 51.15% | NA |
| Indica Intermediate | 786 | 50.80% | 0.40% | 11.20% | 37.66% | NA |
| Temperate Japonica | 767 | 97.00% | 0.00% | 0.13% | 2.87% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 2.20% | 5.56% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101692555 | G -> A | LOC_Os11g04170.1 | synonymous_variant ; p.Lys218Lys; LOW | synonymous_codon | Average:66.42; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| vg1101692555 | G -> DEL | LOC_Os11g04170.1 | N | frameshift_variant | Average:66.42; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |