| Variant ID: vg1212722710 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12722710 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: Unkown |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 268. )
TGTTGTGAGACATTAACCGTGCCAACCACAAGCCAGCGTAGGCAACGGCTTTACCTTTTGTATAGCATGATTCATTACGGGGTGCCAGACTGATAAGCGG[T/C]
GAGAAGTCCGTGGGGGTCGCTGGGGAGTCCATGCCTCTGGTTATATTTATAGAGGGGGTGATTATGATCCAGGAATGGTGCACTATGGTGAGTTGTGTTG
CAACACAACTCACCATAGTGCACCATTCCTGGATCATAATCACCCCCTCTATAAATATAACCAGAGGCATGGACTCCCCAGCGACCCCCACGGACTTCTC[A/G]
CCGCTTATCAGTCTGGCACCCCGTAATGAATCATGCTATACAAAAGGTAAAGCCGTTGCCTACGCTGGCTTGTGGTTGGCACGGTTAATGTCTCACAACA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.60% | 0.00% | 0.04% | 0.36% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.04% | NA |
| All Japonica | 1512 | 98.80% | 0.00% | 0.13% | 1.06% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Temperate Japonica | 767 | 97.70% | 0.00% | 0.26% | 2.09% | 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 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1212722710 | T -> C | LOC_Os12g22540.1 | synonymous_variant ; p.Gly23Gly; LOW | N | Average:53.937; most accessible tissue: Minghui63 young leaf, score: 75.937 | N | N | N | N |
| vg1212722710 | T -> C | LOC_Os12g22530.1 | downstream_gene_variant ; 4256.0bp to feature; MODIFIER | N | Average:53.937; most accessible tissue: Minghui63 young leaf, score: 75.937 | N | N | N | N |