| Variant ID: vg1213095594 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 13095594 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AAATGGTACACATCGGCCTTCTTTTTGCGGATTGAAGATCAACAGGAGTAGCGCAACATACAGAAGAAGCTGTAGATACGGAATCACCAACTACCATTCT[A/G]
TACATATGAAATAGGTGGCGAGTGCTAGTAGGGATCGTAGTTACATCTTTGTCATGCTCCATGTAAAATCCAGGCTTCAGTTCTATCTTCTTGTCTCCAT
ATGGAGACAAGAAGATAGAACTGAAGCCTGGATTTTACATGGAGCATGACAAAGATGTAACTACGATCCCTACTAGCACTCGCCACCTATTTCATATGTA[T/C]
AGAATGGTAGTTGGTGATTCCGTATCTACAGCTTCTTCTGTATGTTGCGCTACTCCTGTTGATCTTCAATCCGCAAAAAGAAGGCCGATGTGTACCATTT
| 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 | 88.60% | 0.00% | 0.55% | 10.85% | NA |
| All Indica | 2759 | 82.00% | 0.00% | 0.83% | 17.14% | NA |
| All Japonica | 1512 | 97.40% | 0.00% | 0.20% | 2.45% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 0.00% | 0.17% | 1.01% | NA |
| Indica II | 465 | 60.40% | 0.00% | 2.37% | 37.20% | NA |
| Indica III | 913 | 82.00% | 0.10% | 0.11% | 17.74% | NA |
| Indica Intermediate | 786 | 81.90% | 0.00% | 1.27% | 16.79% | NA |
| Temperate Japonica | 767 | 95.30% | 0.00% | 0.39% | 4.30% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 0.00% | 0.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1213095594 | A -> DEL | LOC_Os12g23150.1 | N | frameshift_variant | Average:64.725; most accessible tissue: Minghui63 flower, score: 78.614 | N | N | N | N |
| vg1213095594 | A -> G | LOC_Os12g23150.1 | synonymous_variant ; p.Tyr177Tyr; LOW | synonymous_codon | Average:64.725; most accessible tissue: Minghui63 flower, score: 78.614 | N | N | N | N |