| Variant ID: vg0725421359 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25421359 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGGATTTGTCGACCCTCTGAAGCGCCTCCCCCTGCTTAGGGCTTTGGCGCGGAGGAGGTGGAGGAGTACGAGCTCGACGGCGTGGATTCGGCTCCCCGTC[G/A]
TCGCCGCTCACACTCGGAGAGAGGTCGTGCGCTTTTCCTTGCTCGGCCATTAGGCTGAACAAGAAAAACTTGGCACACACGGAAGAGTCTGAGAGCTCAG
CTGAGCTCTCAGACTCTTCCGTGTGTGCCAAGTTTTTCTTGTTCAGCCTAATGGCCGAGCAAGGAAAAGCGCACGACCTCTCTCCGAGTGTGAGCGGCGA[C/T]
GACGGGGAGCCGAATCCACGCCGTCGAGCTCGTACTCCTCCACCTCCTCCGCGCCAAAGCCCTAAGCAGGGGGAGGCGCTTCAGAGGGTCGACAAATCCG
| 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 | 24.80% | 0.40% | 1.14% | 73.74% | NA |
| All Indica | 2759 | 5.90% | 0.60% | 1.23% | 92.28% | NA |
| All Japonica | 1512 | 60.20% | 0.00% | 0.26% | 39.55% | NA |
| Aus | 269 | 3.30% | 0.00% | 1.12% | 95.54% | NA |
| Indica I | 595 | 4.70% | 2.40% | 1.68% | 91.26% | NA |
| Indica II | 465 | 4.50% | 0.00% | 0.00% | 95.48% | NA |
| Indica III | 913 | 7.60% | 0.00% | 0.99% | 91.46% | NA |
| Indica Intermediate | 786 | 5.60% | 0.40% | 1.91% | 92.11% | NA |
| Temperate Japonica | 767 | 89.70% | 0.00% | 0.26% | 10.04% | NA |
| Tropical Japonica | 504 | 13.30% | 0.00% | 0.20% | 86.51% | NA |
| Japonica Intermediate | 241 | 64.30% | 0.00% | 0.41% | 35.27% | NA |
| VI/Aromatic | 96 | 64.60% | 0.00% | 3.12% | 32.29% | NA |
| Intermediate | 90 | 30.00% | 0.00% | 11.11% | 58.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725421359 | G -> DEL | LOC_Os07g42460.1 | N | frameshift_variant | Average:7.82; most accessible tissue: Zhenshan97 flag leaf, score: 13.342 | N | N | N | N |
| vg0725421359 | G -> A | LOC_Os07g42460.1 | synonymous_variant ; p.Asp17Asp; LOW | synonymous_codon | Average:7.82; most accessible tissue: Zhenshan97 flag leaf, score: 13.342 | N | N | N | N |