| Variant ID: vg0512046885 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12046885 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TAGGGTTGCATTTGCAAAAGCAGCATTTAGCAGACATTTGAGAATTTGATAAAACAGTTAAGTAATTAAACAATATTAATCCAACGCTATACAACATACC[C/A]
TGTTGTATAGGCCCAACCATTCTGAACAACCACCCCGGCTGCAAAGTTCTATCTCCAAACCAGGAATGTACCATTCCAAACCAGGAGCTAATCAAATTAT
ATAATTTGATTAGCTCCTGGTTTGGAATGGTACATTCCTGGTTTGGAGATAGAACTTTGCAGCCGGGGTGGTTGTTCAGAATGGTTGGGCCTATACAACA[G/T]
GGTATGTTGTATAGCGTTGGATTAATATTGTTTAATTACTTAACTGTTTTATCAAATTCTCAAATGTCTGCTAAATGCTGCTTTTGCAAATGCAACCCTA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.50% | 2.10% | 5.80% | 9.61% | NA |
| All Indica | 2759 | 81.60% | 3.50% | 6.74% | 8.12% | NA |
| All Japonica | 1512 | 93.90% | 0.00% | 5.29% | 0.79% | NA |
| Aus | 269 | 21.60% | 0.00% | 0.74% | 77.70% | NA |
| Indica I | 595 | 84.50% | 4.40% | 6.72% | 4.37% | NA |
| Indica II | 465 | 92.00% | 4.30% | 2.80% | 0.86% | NA |
| Indica III | 913 | 74.90% | 1.90% | 9.53% | 13.69% | NA |
| Indica Intermediate | 786 | 81.00% | 4.30% | 5.85% | 8.78% | NA |
| Temperate Japonica | 767 | 89.00% | 0.00% | 10.04% | 0.91% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 1.24% | 0.41% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 86.70% | 1.10% | 3.33% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512046885 | C -> DEL | LOC_Os05g20520.1 | N | frameshift_variant | Average:36.021; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
| vg0512046885 | C -> A | LOC_Os05g20520.1 | missense_variant&splice_region_variant ; p.Arg26Met; MODERATE | nonsynonymous_codon ; R26M | Average:36.021; most accessible tissue: Zhenshan97 panicle, score: 67.02 | unknown | unknown | TOLERATED | 0.13 |