| Variant ID: vg0704650217 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 4650217 |
| 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: 354. )
TGGTGCTTTTAGCTGTCACCACTCTGGTGATACCAACGCTCGTGATTGACTCAAGCTTGATGTTGCGGCATGTCACAAGCATGTTGTTGAGCGTGGCAAT[A/T]
ATCTTGGCACACAACTCCTGGAATGTATCCTTTGGTTTCATCTCAACTTGAGCCATGTCGCCCTCGGCTTTGTTGGTTTTGATGGATGGTGACGGTGTTG
CAACACCGTCACCATCCATCAAAACCAACAAAGCCGAGGGCGACATGGCTCAAGTTGAGATGAAACCAAAGGATACATTCCAGGAGTTGTGTGCCAAGAT[T/A]
ATTGCCACGCTCAACAACATGCTTGTGACATGCCGCAACATCAAGCTTGAGTCAATCACGAGCGTTGGTATCACCAGAGTGGTGACAGCTAAAAGCACCA
| 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 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0704650217 | A -> T | LOC_Os07g08940.1 | synonymous_variant ; p.Ile113Ile; LOW | N | Average:56.289; most accessible tissue: Zhenshan97 young leaf, score: 70.625 | N | N | N | N |
| vg0704650217 | A -> T | LOC_Os07g08934.1 | upstream_gene_variant ; 3464.0bp to feature; MODIFIER | N | Average:56.289; most accessible tissue: Zhenshan97 young leaf, score: 70.625 | N | N | N | N |
| vg0704650217 | A -> T | LOC_Os07g08950.1 | upstream_gene_variant ; 2576.0bp to feature; MODIFIER | N | Average:56.289; most accessible tissue: Zhenshan97 young leaf, score: 70.625 | N | N | N | N |