| Variant ID: vg0710993152 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 10993152 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCTTTAAATCAAAAAACAAGGAAGAATTTTCACCATGATGTACAGCTTCTCCAAGCATGGAAAACATTTAAGGAAGCCAAATTGTGTCCAGATTTGGTCC[A/T]
GCAGACTCAAGAACCAAAACCTTCACTGTGCGCAGCGAGGCTGTCGAACTGACGACCATCGTTTCCTGAAGAAAACCAAGACGTACAGCATGTCAAGATG
CATCTTGACATGCTGTACGTCTTGGTTTTCTTCAGGAAACGATGGTCGTCAGTTCGACAGCCTCGCTGCGCACAGTGAAGGTTTTGGTTCTTGAGTCTGC[T/A]
GGACCAAATCTGGACACAATTTGGCTTCCTTAAATGTTTTCCATGCTTGGAGAAGCTGTACATCATGGTGAAAATTCTTCCTTGTTTTTTGATTTAAAGG
| 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 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 95.50% | 4.50% | 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 | 100.00% | 0.00% | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0710993152 | A -> T | LOC_Os07g18600.1 | synonymous_variant ; p.Ala330Ala; LOW | N | Average:44.944; most accessible tissue: Zhenshan97 young leaf, score: 71.497 | N | N | N | N |
| vg0710993152 | A -> T | LOC_Os07g18580.1 | upstream_gene_variant ; 3620.0bp to feature; MODIFIER | N | Average:44.944; most accessible tissue: Zhenshan97 young leaf, score: 71.497 | N | N | N | N |
| vg0710993152 | A -> T | LOC_Os07g18610.1 | upstream_gene_variant ; 4891.0bp to feature; MODIFIER | N | Average:44.944; most accessible tissue: Zhenshan97 young leaf, score: 71.497 | N | N | N | N |
| vg0710993152 | A -> T | LOC_Os07g18590.1 | downstream_gene_variant ; 711.0bp to feature; MODIFIER | N | Average:44.944; most accessible tissue: Zhenshan97 young leaf, score: 71.497 | N | N | N | N |