| Variant ID: vg1105342797 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5342797 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.73, A: 0.28, others allele: 0.00, population size: 222. )
TTCAAACTTCCAACTTTTCCATCACATGAAAACTTTCCTACACAAATAAACTTCTAACTTTTTTCTTCAAACTTCCAATTTTAGTCAAACTTCCAATTTT[A/G]
GCGTGGAACTAAACACAGCCCTACTACAAATCCAAAAGTCTGCCCCTTCAAGCTACTTAGAGGGAGAAAAACACCAATGTTACCATCCTTTAGGTCTCAA
TTGAGACCTAAAGGATGGTAACATTGGTGTTTTTCTCCCTCTAAGTAGCTTGAAGGGGCAGACTTTTGGATTTGTAGTAGGGCTGTGTTTAGTTCCACGC[T/C]
AAAATTGGAAGTTTGACTAAAATTGGAAGTTTGAAGAAAAAAGTTAGAAGTTTATTTGTGTAGGAAAGTTTTCATGTGATGGAAAAGTTGGAAGTTTGAA
| 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 | 82.90% | 16.80% | 0.36% | 0.00% | NA |
| All Indica | 2759 | 93.70% | 6.20% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 66.70% | 33.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 90.70% | 9.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 94.80% | 4.90% | 0.22% | 0.00% | NA |
| Indica III | 913 | 92.60% | 7.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 90.80% | 8.90% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 63.10% | 36.90% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 81.30% | 18.70% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 47.30% | 52.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 10.40% | 78.10% | 11.46% | 0.00% | NA |
| Intermediate | 90 | 76.70% | 20.00% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105342797 | A -> G | LOC_Os11g09970.1 | 3_prime_UTR_variant ; 129.0bp to feature; MODIFIER | silent_mutation | Average:63.027; most accessible tissue: Callus, score: 85.918 | N | N | N | N |
| vg1105342797 | A -> G | LOC_Os11g09960.1 | upstream_gene_variant ; 2292.0bp to feature; MODIFIER | silent_mutation | Average:63.027; most accessible tissue: Callus, score: 85.918 | N | N | N | N |