| Variant ID: vg0725421299 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25421299 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGAGGAGGCGACGCTCCCCATCTCGCCGTTCTCCTGCATCACCTGCGACTGGTGATGCCACGGATTTGTCGACCCTCTGAAGCGCCTCCCCCTGCTTAGG[G/A]
CTTTGGCGCGGAGGAGGTGGAGGAGTACGAGCTCGACGGCGTGGATTCGGCTCCCCGTCGTCGCCGCTCACACTCGGAGAGAGGTCGTGCGCTTTTCCTT
AAGGAAAAGCGCACGACCTCTCTCCGAGTGTGAGCGGCGACGACGGGGAGCCGAATCCACGCCGTCGAGCTCGTACTCCTCCACCTCCTCCGCGCCAAAG[C/T]
CCTAAGCAGGGGGAGGCGCTTCAGAGGGTCGACAAATCCGTGGCATCACCAGTCGCAGGTGATGCAGGAGAACGGCGAGATGGGGAGCGTCGCCTCCTCG
| 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 | 27.70% | 0.10% | 1.69% | 70.50% | NA |
| All Indica | 2759 | 9.70% | 0.10% | 1.49% | 88.69% | NA |
| All Japonica | 1512 | 60.70% | 0.10% | 2.25% | 36.90% | NA |
| Aus | 269 | 5.20% | 0.00% | 0.74% | 94.05% | NA |
| Indica I | 595 | 8.40% | 0.20% | 1.85% | 89.58% | NA |
| Indica II | 465 | 5.60% | 0.00% | 0.43% | 93.98% | NA |
| Indica III | 913 | 13.30% | 0.20% | 1.75% | 84.78% | NA |
| Indica Intermediate | 786 | 9.00% | 0.00% | 1.53% | 89.44% | NA |
| Temperate Japonica | 767 | 90.00% | 0.00% | 0.00% | 10.04% | NA |
| Tropical Japonica | 504 | 14.90% | 0.00% | 6.15% | 78.97% | NA |
| Japonica Intermediate | 241 | 63.50% | 0.80% | 1.24% | 34.44% | NA |
| VI/Aromatic | 96 | 77.10% | 0.00% | 0.00% | 22.92% | NA |
| Intermediate | 90 | 38.90% | 0.00% | 3.33% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725421299 | G -> DEL | LOC_Os07g42460.1 | N | frameshift_variant | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0725421299 | G -> A | LOC_Os07g42460.1 | synonymous_variant ; p.Ser37Ser; LOW | synonymous_codon | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |