| Variant ID: vg1105342851 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5342851 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.66, T: 0.35, others allele: 0.00, population size: 218. )
TAACTTTTTTCTTCAAACTTCCAATTTTAGTCAAACTTCCAATTTTAGCGTGGAACTAAACACAGCCCTACTACAAATCCAAAAGTCTGCCCCTTCAAGC[T/A]
ACTTAGAGGGAGAAAAACACCAATGTTACCATCCTTTAGGTCTCAACCTTCTGAATAATCAAAATGGTGGTGCATCAAGCATCTTCATTGTCATCCTCAT
ATGAGGATGACAATGAAGATGCTTGATGCACCACCATTTTGATTATTCAGAAGGTTGAGACCTAAAGGATGGTAACATTGGTGTTTTTCTCCCTCTAAGT[A/T]
GCTTGAAGGGGCAGACTTTTGGATTTGTAGTAGGGCTGTGTTTAGTTCCACGCTAAAATTGGAAGTTTGACTAAAATTGGAAGTTTGAAGAAAAAAGTTA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.70% | 17.20% | 0.15% | 0.00% | NA |
| All Indica | 2759 | 93.60% | 6.20% | 0.14% | 0.00% | NA |
| All Japonica | 1512 | 66.30% | 33.50% | 0.20% | 0.00% | NA |
| Aus | 269 | 90.70% | 9.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.30% | 1.50% | 0.17% | 0.00% | NA |
| Indica II | 465 | 94.60% | 5.20% | 0.22% | 0.00% | NA |
| Indica III | 913 | 92.40% | 7.40% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 90.80% | 9.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 63.00% | 37.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 81.00% | 18.80% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 46.10% | 53.10% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 10.40% | 89.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 76.70% | 23.30% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105342851 | T -> A | LOC_Os11g09970.1 | 3_prime_UTR_variant ; 75.0bp to feature; MODIFIER | silent_mutation | Average:59.788; most accessible tissue: Zhenshan97 root, score: 72.671 | N | N | N | N |
| vg1105342851 | T -> A | LOC_Os11g09960.1 | upstream_gene_variant ; 2346.0bp to feature; MODIFIER | silent_mutation | Average:59.788; most accessible tissue: Zhenshan97 root, score: 72.671 | N | N | N | N |