| Variant ID: vg0817015679 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015679 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGTAGCTGCCAGCACGTCAGTCCACGCAAACCCCCGCAATCAGAAGCTTGCTCCTCAACGAATTGTCATCCATGCATCCCGAAGCAGTCCGATAGCCCGC[G/A]
TTGCAACAGCTCCAACTCCAATGAGTGCACTACCACAAGGTGTCAATGCTCAATTTCAGCCCCAGCCACCAGCTGACAAGACAGAGGCCAGTATCTGCGT
ACGCAGATACTGGCCTCTGTCTTGTCAGCTGGTGGCTGGGGCTGAAATTGAGCATTGACACCTTGTGGTAGTGCACTCATTGGAGTTGGAGCTGTTGCAA[C/T]
GCGGGCTATCGGACTGCTTCGGGATGCATGGATGACAATTCGTTGAGGAGCAAGCTTCTGATTGCGGGGGTTTGCGTGGACTGACGTGCTGGCAGCTACG
| 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 | 23.50% | 0.30% | 24.71% | 51.42% | NA |
| All Indica | 2759 | 10.70% | 0.00% | 26.68% | 62.63% | NA |
| All Japonica | 1512 | 48.70% | 0.90% | 15.81% | 34.52% | NA |
| Aus | 269 | 16.70% | 0.00% | 38.29% | 44.98% | NA |
| Indica I | 595 | 6.60% | 0.00% | 9.75% | 83.70% | NA |
| Indica II | 465 | 2.60% | 0.00% | 24.73% | 72.69% | NA |
| Indica III | 913 | 18.50% | 0.00% | 39.10% | 42.39% | NA |
| Indica Intermediate | 786 | 9.50% | 0.00% | 26.21% | 64.25% | NA |
| Temperate Japonica | 767 | 68.80% | 0.00% | 10.04% | 21.12% | NA |
| Tropical Japonica | 504 | 23.60% | 2.60% | 18.25% | 55.56% | NA |
| Japonica Intermediate | 241 | 37.30% | 0.40% | 29.05% | 33.20% | NA |
| VI/Aromatic | 96 | 10.40% | 0.00% | 68.75% | 20.83% | NA |
| Intermediate | 90 | 27.80% | 2.20% | 26.67% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015679 | G -> A | LOC_Os08g27910.1 | missense_variant ; p.Val363Ile; MODERATE | nonsynonymous_codon ; V363I | Average:5.77; most accessible tissue: Callus, score: 12.96 | unknown | unknown | TOLERATED | 0.07 |
| vg0817015679 | G -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:5.77; most accessible tissue: Callus, score: 12.96 | N | N | N | N |