| Variant ID: vg1225601283 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25601283 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TTCATTGGGAAAAAGCTCTCAAAGAAGGTAGCATCACGAGACTCCATAATTGTACCAACATGCATGTCCGGTACCTCAGATTTAACTATTGAAAATCTAT[A/G]
GGCAATGCTATGATGAGCATATCCCAGAAAAACACAGTCCACAGTCTTAGGTCCAAGTTTTCGCTTCTTCGTTATTGGTACATTGACTTTCGCCAAGCAC
GTGCTTGGCGAAAGTCAATGTACCAATAACGAAGAAGCGAAAACTTGGACCTAAGACTGTGGACTGTGTTTTTCTGGGATATGCTCATCATAGCATTGCC[T/C]
ATAGATTTTCAATAGTTAAATCTGAGGTACCGGACATGCATGTTGGTACAATTATGGAGTCTCGTGATGCTACCTTCTTTGAGAGCTTTTTCCCAATGAA
| 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 | 53.50% | 0.40% | 5.48% | 40.67% | NA |
| All Indica | 2759 | 40.10% | 0.10% | 1.56% | 58.21% | NA |
| All Japonica | 1512 | 86.40% | 0.60% | 12.90% | 0.07% | NA |
| Aus | 269 | 0.70% | 0.40% | 2.97% | 95.91% | NA |
| Indica I | 595 | 86.40% | 0.00% | 0.84% | 12.77% | NA |
| Indica II | 465 | 14.00% | 0.00% | 1.51% | 84.52% | NA |
| Indica III | 913 | 26.40% | 0.00% | 1.75% | 71.85% | NA |
| Indica Intermediate | 786 | 36.50% | 0.40% | 1.91% | 61.20% | NA |
| Temperate Japonica | 767 | 86.30% | 0.70% | 13.04% | 0.00% | NA |
| Tropical Japonica | 504 | 96.00% | 0.00% | 3.97% | 0.00% | NA |
| Japonica Intermediate | 241 | 66.80% | 1.70% | 31.12% | 0.41% | NA |
| VI/Aromatic | 96 | 59.40% | 4.20% | 10.42% | 26.04% | NA |
| Intermediate | 90 | 60.00% | 1.10% | 3.33% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225601283 | A -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:12.867; most accessible tissue: Zhenshan97 flower, score: 23.247 | N | N | N | N |
| vg1225601283 | A -> G | LOC_Os12g41280.1 | missense_variant ; p.Tyr694His; MODERATE | nonsynonymous_codon ; Y694H | Average:12.867; most accessible tissue: Zhenshan97 flower, score: 23.247 | unknown | unknown | DELETERIOUS | 0.00 |