| Variant ID: vg1115079735 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 15079735 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TCTGAATTTCTGTCTTTGTTTCTGAATTTCTGTCTCCCACAAGGTTACCTTGGTTATACTGCACAATATCCAAATTTGCTATACACGGTCTCTCATATTT[A/G]
TTAATTTCTTCAGTTTGTCCAATTTCCCATATGAATTTTGAAAAATAAGAAACACCTTCCATGGGAATACCAATATATCTGTTACTGTCCAATGTCTATT
AATAGACATTGGACAGTAACAGATATATTGGTATTCCCATGGAAGGTGTTTCTTATTTTTCAAAATTCATATGGGAAATTGGACAAACTGAAGAAATTAA[T/C]
AAATATGAGAGACCGTGTATAGCAAATTTGGATATTGTGCAGTATAACCAAGGTAACCTTGTGGGAGACAGAAATTCAGAAACAAAGACAGAAATTCAGA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.40% | 0.40% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 99.10% | 0.70% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.20% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.40% | 0.22% | 0.00% | NA |
| Indica III | 913 | 98.10% | 1.50% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 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 | 99.60% | 0.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1115079735 | A -> G | LOC_Os11g26340.1 | downstream_gene_variant ; 3769.0bp to feature; MODIFIER | N | Average:6.16; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |
| vg1115079735 | A -> G | LOC_Os11g26360.1 | downstream_gene_variant ; 3095.0bp to feature; MODIFIER | N | Average:6.16; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |
| vg1115079735 | A -> G | LOC_Os11g26350.1 | intron_variant ; MODIFIER | N | Average:6.16; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |