| Variant ID: vg1223515363 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 23515363 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 204. )
CTGTCATAAGCTTTGATGATTTTGATGTACTTTCCATCATAGAAGAATACTATGTTAGCCCCAATAGTTCTGCTTACAATTGATTTGAAGTTATATTCAG[T/A]
TGAAGCCATCCATAAGACAAAAAAAAAGTTGTCATTTCTAGTTACTGAATTTTGCGTTCTGTTTTTTGTTTTCTTGGTTCAGAAAGATGTACCCTGACCT
AGGTCAGGGTACATCTTTCTGAACCAAGAAAACAAAAAACAGAACGCAAAATTCAGTAACTAGAAATGACAACTTTTTTTTTGTCTTATGGATGGCTTCA[A/T]
CTGAATATAACTTCAAATCAATTGTAAGCAGAACTATTGGGGCTAACATAGTATTCTTCTATGATGGAAAGTACATCAAAATCATCAAAGCTTATGACAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.70% | 1.10% | 0.19% | 0.00% | NA |
| All Indica | 2759 | 98.30% | 1.50% | 0.22% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.20% | 0.07% | 0.00% | NA |
| Aus | 269 | 97.80% | 1.50% | 0.74% | 0.00% | NA |
| Indica I | 595 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.70% | 1.20% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 97.20% | 2.20% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 99.50% | 0.40% | 0.13% | 0.00% | 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 | 99.00% | 1.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1223515363 | T -> A | LOC_Os12g38310.1 | upstream_gene_variant ; 1289.0bp to feature; MODIFIER | silent_mutation | Average:63.719; most accessible tissue: Minghui63 root, score: 88.175 | N | N | N | N |
| vg1223515363 | T -> A | LOC_Os12g38280.1 | downstream_gene_variant ; 4782.0bp to feature; MODIFIER | silent_mutation | Average:63.719; most accessible tissue: Minghui63 root, score: 88.175 | N | N | N | N |
| vg1223515363 | T -> A | LOC_Os12g38290.1 | downstream_gene_variant ; 1886.0bp to feature; MODIFIER | silent_mutation | Average:63.719; most accessible tissue: Minghui63 root, score: 88.175 | N | N | N | N |
| vg1223515363 | T -> A | LOC_Os12g38320.1 | downstream_gene_variant ; 4605.0bp to feature; MODIFIER | silent_mutation | Average:63.719; most accessible tissue: Minghui63 root, score: 88.175 | N | N | N | N |
| vg1223515363 | T -> A | LOC_Os12g38300.1 | intron_variant ; MODIFIER | silent_mutation | Average:63.719; most accessible tissue: Minghui63 root, score: 88.175 | N | N | N | N |