| Variant ID: vg1200521280 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 521280 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGATCGGAATTTTCACATGTTGCCTATTTTGATCTTGGAACGAAATTTCATTGACCCATGTCTAACACGACATAATCCTTCTCTTCGATTCTCATCGGTA[G/C]
CGGCGGCGCATCAACGGCGACGATGCAGCCTTCTCTCTCCAAAGGCGCCATCGCCGCCTCCTCCTCCTCCTCCTCGCCACCTTTGGCGTACAGCACGTCC
GGACGTGCTGTACGCCAAAGGTGGCGAGGAGGAGGAGGAGGAGGCGGCGATGGCGCCTTTGGAGAGAGAAGGCTGCATCGTCGCCGTTGATGCGCCGCCG[C/G]
TACCGATGAGAATCGAAGAGAAGGATTATGTCGTGTTAGACATGGGTCAATGAAATTTCGTTCCAAGATCAAAATAGGCAACATGTGAAAATTCCGATCT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(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 | 100.00% | 0.00% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 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 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1200521280 | G -> C | LOC_Os12g01890.1 | missense_variant ; p.Leu402Val; MODERATE | N | Average:63.756; most accessible tissue: Zhenshan97 flower, score: 83.172 | N | N | N | N |
| vg1200521280 | G -> C | LOC_Os12g01880.1 | downstream_gene_variant ; 4225.0bp to feature; MODIFIER | N | Average:63.756; most accessible tissue: Zhenshan97 flower, score: 83.172 | N | N | N | N |
| vg1200521280 | G -> C | LOC_Os12g01900.1 | downstream_gene_variant ; 2771.0bp to feature; MODIFIER | N | Average:63.756; most accessible tissue: Zhenshan97 flower, score: 83.172 | N | N | N | N |