| Variant ID: vg0817015182 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015182 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTTTTAGCTAATGGAGGTAGAGTGTCTGATAGTGAAGATTCAGATCAAGTCTCCTCAGATGATGAAGGTGCGAAGCCTCCCCAAGGTTTTAACCAGAATA[A/G]
AATAGAACTTAAGGCATGCTCTCGTTGTGGAGAAATCGGTCATGTTGCCAGCTCGTGTGCCTCTATATGCGTTCATTGTGAGGAAGACCATCCACCCGAC
GTCGGGTGGATGGTCTTCCTCACAATGAACGCATATAGAGGCACACGAGCTGGCAACATGACCGATTTCTCCACAACGAGAGCATGCCTTAAGTTCTATT[T/C]
TATTCTGGTTAAAACCTTGGGGAGGCTTCGCACCTTCATCATCTGAGGAGACTTGATCTGAATCTTCACTATCAGACACTCTACCTCCATTAGCTAAAAG
| 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 | 17.90% | 0.60% | 13.82% | 67.67% | NA |
| All Indica | 2759 | 1.90% | 0.30% | 15.01% | 82.78% | NA |
| All Japonica | 1512 | 51.10% | 0.10% | 8.07% | 40.81% | NA |
| Aus | 269 | 0.40% | 1.50% | 14.50% | 83.64% | NA |
| Indica I | 595 | 3.90% | 0.00% | 4.87% | 91.26% | NA |
| Indica II | 465 | 0.90% | 0.60% | 12.47% | 86.02% | NA |
| Indica III | 913 | 0.80% | 0.70% | 27.60% | 70.97% | NA |
| Indica Intermediate | 786 | 2.30% | 0.00% | 9.54% | 88.17% | NA |
| Temperate Japonica | 767 | 69.10% | 0.00% | 4.82% | 26.08% | NA |
| Tropical Japonica | 504 | 29.40% | 0.00% | 7.54% | 63.10% | NA |
| Japonica Intermediate | 241 | 39.00% | 0.40% | 19.50% | 41.08% | NA |
| VI/Aromatic | 96 | 1.00% | 12.50% | 65.62% | 20.83% | NA |
| Intermediate | 90 | 23.30% | 2.20% | 16.67% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015182 | A -> G | LOC_Os08g27910.1 | missense_variant ; p.Lys197Arg; MODERATE | nonsynonymous_codon ; K197R | Average:6.995; most accessible tissue: Minghui63 panicle, score: 16.27 | unknown | unknown | DELETERIOUS | 0.04 |
| vg0817015182 | A -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:6.995; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |