| Variant ID: vg1115080722 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 15080722 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AACGGCGCTAATTTGCAAGGAACAACAAGTACTACCCGGCAAAATATTTCTTCACAACATCTTAGGAATGTTGCTAGAAATTTTGTACGGTCCCGAACTG[A/G]
TCAGGTAATTACAAATCTTCAGCAAGCTGCTATGTTGAAATGATCTTTTGCAAAAAAATTTACAATATGTTTTCCTGCTCATGGTCTGTTTGTAAAAAAA
TTTTTTTACAAACAGACCATGAGCAGGAAAACATATTGTAAATTTTTTTGCAAAAGATCATTTCAACATAGCAGCTTGCTGAAGATTTGTAATTACCTGA[T/C]
CAGTTCGGGACCGTACAAAATTTCTAGCAACATTCCTAAGATGTTGTGAAGAAATATTTTGCCGGGTAGTACTTGTTGTTCCTTGCAAATTAGCGCCGTT
| 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 | 69.60% | 0.10% | 10.50% | 19.81% | NA |
| All Indica | 2759 | 50.10% | 0.00% | 17.43% | 32.51% | NA |
| All Japonica | 1512 | 98.70% | 0.00% | 0.20% | 1.12% | NA |
| Aus | 269 | 94.80% | 0.00% | 1.12% | 4.09% | NA |
| Indica I | 595 | 37.80% | 0.00% | 10.76% | 51.43% | NA |
| Indica II | 465 | 48.20% | 0.00% | 25.59% | 26.24% | NA |
| Indica III | 913 | 54.50% | 0.00% | 19.06% | 26.40% | NA |
| Indica Intermediate | 786 | 55.20% | 0.00% | 15.78% | 29.01% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.26% | 1.17% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.20% | 0.60% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 75.60% | 2.20% | 10.00% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1115080722 | A -> DEL | LOC_Os11g26350.1 | N | frameshift_variant | Average:4.876; most accessible tissue: Callus, score: 8.966 | N | N | N | N |
| vg1115080722 | A -> G | LOC_Os11g26350.1 | missense_variant ; p.Asp180Gly; MODERATE | nonsynonymous_codon ; D180G | Average:4.876; most accessible tissue: Callus, score: 8.966 | unknown | unknown | DELETERIOUS | 0.00 |