| Variant ID: vg0136518367 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36518367 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGAAATCTCTCAACTTCTTGTTGGAACATTATTCGAATTGCAAGGTTGAGAGAATCTGAATCCATTTGGCTCCCAATCTTTATAGTTTCTTGGATGTTTC[G/A]
TAGCGTCAATGATATTATGAAAGGATGGGAGCTCTGCAGCCATGTTTTTCTGAAATAAACCATGGATAAAAATGAATGTCAGATTTGGTGGGGTGAGATG
CATCTCACCCCACCAAATCTGACATTCATTTTTATCCATGGTTTATTTCAGAAAAACATGGCTGCAGAGCTCCCATCCTTTCATAATATCATTGACGCTA[C/T]
GAAACATCCAAGAAACTATAAAGATTGGGAGCCAAATGGATTCAGATTCTCTCAACCTTGCAATTCGAATAATGTTCCAACAAGAAGTTGAGAGATTTCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.90% | 0.10% | 8.42% | 54.57% | NA |
| All Indica | 2759 | 4.50% | 0.00% | 6.13% | 89.42% | NA |
| All Japonica | 1512 | 97.20% | 0.10% | 1.19% | 1.59% | NA |
| Aus | 269 | 1.10% | 1.50% | 74.72% | 22.68% | NA |
| Indica I | 595 | 1.80% | 0.00% | 5.55% | 92.61% | NA |
| Indica II | 465 | 4.50% | 0.00% | 2.15% | 93.33% | NA |
| Indica III | 913 | 3.30% | 0.00% | 7.67% | 89.05% | NA |
| Indica Intermediate | 786 | 7.80% | 0.00% | 7.12% | 85.11% | NA |
| Temperate Japonica | 767 | 98.80% | 0.00% | 0.26% | 0.91% | NA |
| Tropical Japonica | 504 | 96.80% | 0.20% | 0.40% | 2.58% | NA |
| Japonica Intermediate | 241 | 92.50% | 0.00% | 5.81% | 1.66% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 4.17% | 3.12% | NA |
| Intermediate | 90 | 66.70% | 0.00% | 6.67% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136518367 | G -> A | LOC_Os01g63040.1 | stop_gained ; p.Arg644*; HIGH | stop_gained | Average:4.669; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0136518367 | G -> DEL | LOC_Os01g63040.1 | N | frameshift_variant | Average:4.669; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |