| Variant ID: vg0512045340 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12045340 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CCGGAGGATCCGCTTGAGCTGGGGCAACTTCTTTCTCCACCACACGAACCTTTGGCGCCAGTTGATAGCGAGGGACAAATAGAGCTCTCTTCCTTGCGGT[A/G]
AGACGAATCCTGGCCTTCTGCGGCGGTGCTTCTCCCTTCAATGCGGCTAATTCCTTCTCCAAACGATCCACCTTGTCTTCTAGCTTGCAAATCTTACCAC
GTGGTAAGATTTGCAAGCTAGAAGACAAGGTGGATCGTTTGGAGAAGGAATTAGCCGCATTGAAGGGAGAAGCACCGCCGCAGAAGGCCAGGATTCGTCT[T/C]
ACCGCAAGGAAGAGAGCTCTATTTGTCCCTCGCTATCAACTGGCGCCAAAGGTTCGTGTGGTGGAGAAAGAAGTTGCCCCAGCTCAAGCGGATCCTCCGG
| 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 | 82.40% | 0.10% | 6.20% | 11.36% | NA |
| All Indica | 2759 | 86.40% | 0.10% | 8.30% | 5.18% | NA |
| All Japonica | 1512 | 84.90% | 0.00% | 3.17% | 11.97% | NA |
| Aus | 269 | 21.20% | 0.00% | 3.35% | 75.46% | NA |
| Indica I | 595 | 92.30% | 0.00% | 7.56% | 0.17% | NA |
| Indica II | 465 | 97.60% | 0.00% | 0.86% | 1.51% | NA |
| Indica III | 913 | 76.70% | 0.30% | 12.71% | 10.30% | NA |
| Indica Intermediate | 786 | 86.60% | 0.00% | 8.14% | 5.22% | NA |
| Temperate Japonica | 767 | 72.50% | 0.00% | 5.61% | 21.90% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.20% | 0.60% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.00% | 1.66% | 4.15% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 84.40% | 1.10% | 4.44% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512045340 | A -> DEL | LOC_Os05g20520.1 | N | frameshift_variant | Average:18.155; most accessible tissue: Minghui63 young leaf, score: 24.836 | N | N | N | N |
| vg0512045340 | A -> G | LOC_Os05g20520.1 | synonymous_variant ; p.Leu214Leu; LOW | synonymous_codon | Average:18.155; most accessible tissue: Minghui63 young leaf, score: 24.836 | N | N | N | N |