| Variant ID: vg0725421242 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25421242 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTAGGAGCGCGCCAGCAGCCTGAAGCGCACCCTGAGGCGTGCTGCCGTCGCCGTAGACGAGGAGGCGACGCTCCCCATCTCGCCGTTCTCCTGCATCACC[T/A]
GCGACTGGTGATGCCACGGATTTGTCGACCCTCTGAAGCGCCTCCCCCTGCTTAGGGCTTTGGCGCGGAGGAGGTGGAGGAGTACGAGCTCGACGGCGTG
CACGCCGTCGAGCTCGTACTCCTCCACCTCCTCCGCGCCAAAGCCCTAAGCAGGGGGAGGCGCTTCAGAGGGTCGACAAATCCGTGGCATCACCAGTCGC[A/T]
GGTGATGCAGGAGAACGGCGAGATGGGGAGCGTCGCCTCCTCGTCTACGGCGACGGCAGCACGCCTCAGGGTGCGCTTCAGGCTGCTGGCGCGCTCCTAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 26.90% | 0.30% | 1.44% | 71.39% | NA |
| All Indica | 2759 | 7.90% | 0.00% | 1.30% | 90.79% | NA |
| All Japonica | 1512 | 61.80% | 0.90% | 1.85% | 35.38% | NA |
| Aus | 269 | 3.00% | 0.00% | 1.12% | 95.91% | NA |
| Indica I | 595 | 7.10% | 0.00% | 0.67% | 92.27% | NA |
| Indica II | 465 | 4.70% | 0.00% | 0.86% | 94.41% | NA |
| Indica III | 913 | 10.40% | 0.00% | 1.86% | 87.73% | NA |
| Indica Intermediate | 786 | 7.50% | 0.00% | 1.40% | 91.09% | NA |
| Temperate Japonica | 767 | 89.70% | 0.10% | 0.13% | 10.04% | NA |
| Tropical Japonica | 504 | 21.00% | 0.00% | 4.56% | 74.40% | NA |
| Japonica Intermediate | 241 | 58.50% | 5.40% | 1.66% | 34.44% | NA |
| VI/Aromatic | 96 | 76.00% | 0.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0725421242 | T -> DEL | LOC_Os07g42460.1 | N | frameshift_variant | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0725421242 | T -> A | LOC_Os07g42460.1 | synonymous_variant ; p.Ala56Ala; LOW | synonymous_codon | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |