| Variant ID: vg0724211269 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 24211269 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 254. )
TCTCGTGTTTTTTTTTCTCTCTTTTTTTTTCATTTCTCTTCGCGCGCGGAAACTGTTTCTTGTTACTCTTTTGATCCGGTCGCGTTTTTCTCTTTCACTT[T/A]
TTATTTCTTTTCACCTCATGGCAGTGGCGTGTTCATCGCCTCATCATGCATCTTCTATATCTTTCTTGTTGGTTTCCTCGGAAACTGTTCCTTGTAACTC
GAGTTACAAGGAACAGTTTCCGAGGAAACCAACAAGAAAGATATAGAAGATGCATGATGAGGCGATGAACACGCCACTGCCATGAGGTGAAAAGAAATAA[A/T]
AAGTGAAAGAGAAAAACGCGACCGGATCAAAAGAGTAACAAGAAACAGTTTCCGCGCGCGAAGAGAAATGAAAAAAAAAGAGAGAAAAAAAAACACGAGA
| 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 | 87.20% | 12.70% | 0.13% | 0.00% | NA |
| All Indica | 2759 | 78.30% | 21.50% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 98.50% | 1.30% | 0.17% | 0.00% | NA |
| Indica II | 465 | 81.70% | 18.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 61.20% | 38.40% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 80.90% | 19.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 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 | 93.30% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0724211269 | T -> A | LOC_Os07g40370.1 | upstream_gene_variant ; 3304.0bp to feature; MODIFIER | silent_mutation | Average:52.693; most accessible tissue: Callus, score: 93.754 | N | N | N | N |
| vg0724211269 | T -> A | LOC_Os07g40390.1 | downstream_gene_variant ; 4609.0bp to feature; MODIFIER | silent_mutation | Average:52.693; most accessible tissue: Callus, score: 93.754 | N | N | N | N |
| vg0724211269 | T -> A | LOC_Os07g40380.1 | intron_variant ; MODIFIER | silent_mutation | Average:52.693; most accessible tissue: Callus, score: 93.754 | N | N | N | N |