| Variant ID: vg1225599699 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25599699 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TTCAATCGTCTTTTCACATGTCTAGACGATTTCATATTATCCTTAGAACTATTCACTTTGACAATTACCGTTTGATTGTCACAGTTCATAAGGATAGCCG[A/G]
CACCGGTTTTTCAACAACAGGCAGATCCATTAATAGATCACGCAGCCATTCTGCCTCAACAGTAGCAGTATCCAGTGCCGTTAGCTCTGCTTCCATGGTT
AACCATGGAAGCAGAGCTAACGGCACTGGATACTGCTACTGTTGAGGCAGAATGGCTGCGTGATCTATTAATGGATCTGCCTGTTGTTGAAAAACCGGTG[T/C]
CGGCTATCCTTATGAACTGTGACAATCAAACGGTAATTGTCAAAGTGAATAGTTCTAAGGATAATATGAAATCGTCTAGACATGTGAAAAGACGATTGAA
| 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 | 58.70% | 0.40% | 4.68% | 36.23% | NA |
| All Indica | 2759 | 41.10% | 0.70% | 7.87% | 50.34% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.07% | NA |
| Aus | 269 | 1.10% | 0.00% | 0.37% | 98.51% | NA |
| Indica I | 595 | 87.60% | 0.30% | 1.01% | 11.09% | NA |
| Indica II | 465 | 15.50% | 1.90% | 11.61% | 70.97% | NA |
| Indica III | 913 | 27.20% | 0.50% | 12.49% | 59.80% | NA |
| Indica Intermediate | 786 | 37.20% | 0.50% | 5.47% | 56.87% | 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% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 70.80% | 0.00% | 0.00% | 29.17% | NA |
| Intermediate | 90 | 64.40% | 0.00% | 3.33% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225599699 | A -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:13.073; most accessible tissue: Zhenshan97 flag leaf, score: 27.583 | N | N | N | N |
| vg1225599699 | A -> G | LOC_Os12g41280.1 | missense_variant ; p.Ser1222Pro; MODERATE | nonsynonymous_codon ; S1222P | Average:13.073; most accessible tissue: Zhenshan97 flag leaf, score: 27.583 | unknown | unknown | TOLERATED | 1.00 |