| Variant ID: vg0817016017 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17016017 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATCGACCTCCACATTACCGCCAATTTACACGAAGCAGACATTCCAATCGTATTGTGGTCACTGGAGCAAACGCTGTACCCGTGAGGCCTCGTGTTAATCA[G/A]
AACCCATAGCAGAAACAATGCACCAGTGCTCCTCCTGCTGCACCTGACTCTGCAATAAATCATAGCAACCATTCTCTGCACCGACAGCCTTAGCAAAGAA
TTCTTTGCTAAGGCTGTCGGTGCAGAGAATGGTTGCTATGATTTATTGCAGAGTCAGGTGCAGCAGGAGGAGCACTGGTGCATTGTTTCTGCTATGGGTT[C/T]
TGATTAACACGAGGCCTCACGGGTACAGCGTTTGCTCCAGTGACCACAATACGATTGGAATGTCTGCTTCGTGTAAATTGGCGGTAATGTGGAGGTCGAT
| 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 | 34.10% | 0.40% | 16.38% | 49.11% | NA |
| All Indica | 2759 | 17.40% | 0.60% | 22.51% | 59.44% | NA |
| All Japonica | 1512 | 62.60% | 0.10% | 3.90% | 33.33% | NA |
| Aus | 269 | 25.70% | 0.00% | 30.11% | 44.24% | NA |
| Indica I | 595 | 7.60% | 0.20% | 10.08% | 82.18% | NA |
| Indica II | 465 | 9.90% | 1.50% | 21.72% | 66.88% | NA |
| Indica III | 913 | 28.00% | 0.50% | 31.87% | 39.54% | NA |
| Indica Intermediate | 786 | 17.00% | 0.50% | 21.50% | 60.94% | NA |
| Temperate Japonica | 767 | 77.40% | 0.10% | 1.56% | 20.86% | NA |
| Tropical Japonica | 504 | 38.90% | 0.20% | 7.94% | 52.98% | NA |
| Japonica Intermediate | 241 | 65.10% | 0.00% | 2.90% | 31.95% | NA |
| VI/Aromatic | 96 | 76.00% | 1.00% | 2.08% | 20.83% | NA |
| Intermediate | 90 | 44.40% | 1.10% | 12.22% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817016017 | G -> A | LOC_Os08g27910.1 | synonymous_variant ; p.Gln475Gln; LOW | synonymous_codon | Average:7.824; most accessible tissue: Callus, score: 15.831 | N | N | N | N |
| vg0817016017 | G -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:7.824; most accessible tissue: Callus, score: 15.831 | N | N | N | N |