| Variant ID: vg1212722683 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12722683 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 277. )
GCAATTAAAGACAGGTTCGTGAGCTACTGTTGTGAGACATTAACCGTGCCAACCACAAGCCAGCGTAGGCAACGGCTTTACCTTTTGTATAGCATGATTC[A/T]
TTACGGGGTGCCAGACTGATAAGCGGTGAGAAGTCCGTGGGGGTCGCTGGGGAGTCCATGCCTCTGGTTATATTTATAGAGGGGGTGATTATGATCCAGG
CCTGGATCATAATCACCCCCTCTATAAATATAACCAGAGGCATGGACTCCCCAGCGACCCCCACGGACTTCTCACCGCTTATCAGTCTGGCACCCCGTAA[T/A]
GAATCATGCTATACAAAAGGTAAAGCCGTTGCCTACGCTGGCTTGTGGTTGGCACGGTTAATGTCTCACAACAGTAGCTCACGAACCTGTCTTTAATTGC
| 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 | 99.60% | 0.30% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 99.10% | 0.70% | 0.20% | 0.00% | 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 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.10% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.90% | 4.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1212722683 | A -> T | LOC_Os12g22530.1 | downstream_gene_variant ; 4229.0bp to feature; MODIFIER | silent_mutation | Average:51.519; most accessible tissue: Minghui63 panicle, score: 74.563 | N | N | N | N |
| vg1212722683 | A -> T | LOC_Os12g22540.1 | intron_variant ; MODIFIER | silent_mutation | Average:51.519; most accessible tissue: Minghui63 panicle, score: 74.563 | N | N | N | N |