| Variant ID: vg0725421224 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25421224 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGACGACAGGCGGGTGTCGTAGGAGCGCGCCAGCAGCCTGAAGCGCACCCTGAGGCGTGCTGCCGTCGCCGTAGACGAGGAGGCGACGCTCCCCATCTCG[C/T]
CGTTCTCCTGCATCACCTGCGACTGGTGATGCCACGGATTTGTCGACCCTCTGAAGCGCCTCCCCCTGCTTAGGGCTTTGGCGCGGAGGAGGTGGAGGAG
CTCCTCCACCTCCTCCGCGCCAAAGCCCTAAGCAGGGGGAGGCGCTTCAGAGGGTCGACAAATCCGTGGCATCACCAGTCGCAGGTGATGCAGGAGAACG[G/A]
CGAGATGGGGAGCGTCGCCTCCTCGTCTACGGCGACGGCAGCACGCCTCAGGGTGCGCTTCAGGCTGCTGGCGCGCTCCTACGACACCCGCCTGTCGTCC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.70% | 0.10% | 1.46% | 70.72% | NA |
| All Indica | 2759 | 8.20% | 0.00% | 1.88% | 89.85% | NA |
| All Japonica | 1512 | 64.00% | 0.30% | 0.79% | 34.99% | NA |
| Aus | 269 | 3.70% | 0.00% | 0.37% | 95.91% | NA |
| Indica I | 595 | 6.60% | 0.20% | 1.01% | 92.27% | NA |
| Indica II | 465 | 4.90% | 0.00% | 0.86% | 94.19% | NA |
| Indica III | 913 | 11.20% | 0.00% | 3.40% | 85.43% | NA |
| Indica Intermediate | 786 | 8.00% | 0.00% | 1.40% | 90.59% | NA |
| Temperate Japonica | 767 | 88.40% | 0.50% | 1.43% | 9.65% | NA |
| Tropical Japonica | 504 | 26.40% | 0.00% | 0.00% | 73.61% | NA |
| Japonica Intermediate | 241 | 64.70% | 0.00% | 0.41% | 34.85% | NA |
| VI/Aromatic | 96 | 72.90% | 0.00% | 3.12% | 23.96% | NA |
| Intermediate | 90 | 40.00% | 0.00% | 1.11% | 58.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725421224 | C -> DEL | LOC_Os07g42460.1 | N | frameshift_variant | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0725421224 | C -> T | LOC_Os07g42460.1 | synonymous_variant ; p.Arg62Arg; LOW | synonymous_codon | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |