| Variant ID: vg0420971615 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20971615 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGGATGAAGTGGAATTCATAACCCTCTTATATCATCAAATGGCTATGCGCTATCCAGAACTCAAATCTAGTTCCCAGGTAGCTGTCATATCACCATACAG[G/A]
CATCAGGTGAAGCTCTTGAAGGACCATTTTCGGTCGACCTTCGGTGATCAGTCTAAGGAAGTGATAGACGTAAATACAGTTGATGGATTCCAGGTTTGTT
AACAAACCTGGAATCCATCAACTGTATTTACGTCTATCACTTCCTTAGACTGATCACCGAAGGTCGACCGAAAATGGTCCTTCAAGAGCTTCACCTGATG[C/T]
CTGTATGGTGATATGACAGCTACCTGGGAACTAGATTTGAGTTCTGGATAGCGCATAGCCATTTGATGATATAAGAGGGTTATGAATTCCACTTCATCCT
| 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 | 65.70% | 2.70% | 0.83% | 30.79% | NA |
| All Indica | 2759 | 45.90% | 0.80% | 1.20% | 52.05% | NA |
| All Japonica | 1512 | 93.00% | 6.70% | 0.20% | 0.13% | NA |
| Aus | 269 | 98.10% | 0.00% | 0.37% | 1.49% | NA |
| Indica I | 595 | 77.60% | 0.00% | 0.50% | 21.85% | NA |
| Indica II | 465 | 19.40% | 0.90% | 1.94% | 77.85% | NA |
| Indica III | 913 | 44.10% | 1.40% | 0.88% | 53.56% | NA |
| Indica Intermediate | 786 | 39.70% | 0.80% | 1.65% | 57.89% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 82.50% | 16.70% | 0.60% | 0.20% | NA |
| Japonica Intermediate | 241 | 92.90% | 7.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 80.00% | 3.30% | 2.22% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420971615 | G -> DEL | LOC_Os04g34670.1 | N | frameshift_variant | Average:6.644; most accessible tissue: Zhenshan97 flower, score: 15.748 | N | N | N | N |
| vg0420971615 | G -> A | LOC_Os04g34670.1 | synonymous_variant ; p.Arg589Arg; LOW | synonymous_codon | Average:6.644; most accessible tissue: Zhenshan97 flower, score: 15.748 | N | N | N | N |