| Variant ID: vg0329361593 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 29361593 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGGCGGTGTGCCTTGCGGCCCACCTCCACCATGGCCTCCACCGAGCGTCGCCCCTCTTCGACACGCGCCCATGCGGCGTCGAGCTCCGCCCGCTCTGCTT[G/A]
CAGGGCCTCCACCTGGGCACTTAACCCGTCCAACACCGTGGTGTTTGCGATGGCCAAGGCCTGCAGAAGGGGTTCTGCGCTCAGTGGAGCAACGGAAGGC
GCCTTCCGTTGCTCCACTGAGCGCAGAACCCCTTCTGCAGGCCTTGGCCATCGCAAACACCACGGTGTTGGACGGGTTAAGTGCCCAGGTGGAGGCCCTG[C/T]
AAGCAGAGCGGGCGGAGCTCGACGCCGCATGGGCGCGTGTCGAAGAGGGGCGACGCTCGGTGGAGGCCATGGTGGAGGTGGGCCGCAAGGCACACCGCCG
| 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 | 56.80% | 0.50% | 2.07% | 40.69% | NA |
| All Indica | 2759 | 37.90% | 0.80% | 2.86% | 58.43% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.00% | 0.46% | NA |
| Aus | 269 | 1.50% | 0.00% | 5.58% | 92.94% | NA |
| Indica I | 595 | 53.10% | 0.00% | 1.51% | 45.38% | NA |
| Indica II | 465 | 39.60% | 0.20% | 3.44% | 56.77% | NA |
| Indica III | 913 | 27.80% | 2.00% | 2.74% | 67.47% | NA |
| Indica Intermediate | 786 | 37.20% | 0.40% | 3.69% | 58.78% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 70.80% | 0.00% | 1.04% | 28.12% | NA |
| Intermediate | 90 | 66.70% | 0.00% | 3.33% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0329361593 | G -> A | LOC_Os03g51320.1 | stop_gained ; p.Gln591*; HIGH | stop_gained | Average:31.615; most accessible tissue: Zhenshan97 flower, score: 70.106 | N | N | N | N |
| vg0329361593 | G -> DEL | LOC_Os03g51320.1 | N | frameshift_variant | Average:31.615; most accessible tissue: Zhenshan97 flower, score: 70.106 | N | N | N | N |