| Variant ID: vg0725421377 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25421377 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GAAGCGCCTCCCCCTGCTTAGGGCTTTGGCGCGGAGGAGGTGGAGGAGTACGAGCTCGACGGCGTGGATTCGGCTCCCCGTCGTCGCCGCTCACACTCGG[A/C]
GAGAGGTCGTGCGCTTTTCCTTGCTCGGCCATTAGGCTGAACAAGAAAAACTTGGCACACACGGAAGAGTCTGAGAGCTCAGAAAACACACGCTGAGCCC
GGGCTCAGCGTGTGTTTTCTGAGCTCTCAGACTCTTCCGTGTGTGCCAAGTTTTTCTTGTTCAGCCTAATGGCCGAGCAAGGAAAAGCGCACGACCTCTC[T/G]
CCGAGTGTGAGCGGCGACGACGGGGAGCCGAATCCACGCCGTCGAGCTCGTACTCCTCCACCTCCTCCGCGCCAAAGCCCTAAGCAGGGGGAGGCGCTTC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 25.80% | 0.20% | 3.11% | 70.95% | NA |
| All Indica | 2759 | 6.90% | 0.30% | 3.99% | 88.87% | NA |
| All Japonica | 1512 | 60.60% | 0.00% | 1.98% | 37.37% | NA |
| Aus | 269 | 2.20% | 0.00% | 0.74% | 97.03% | NA |
| Indica I | 595 | 11.60% | 0.00% | 0.34% | 88.07% | NA |
| Indica II | 465 | 5.40% | 0.00% | 0.65% | 93.98% | NA |
| Indica III | 913 | 4.30% | 0.80% | 8.87% | 86.09% | NA |
| Indica Intermediate | 786 | 7.10% | 0.10% | 3.05% | 89.69% | NA |
| Temperate Japonica | 767 | 90.00% | 0.00% | 0.00% | 10.04% | NA |
| Tropical Japonica | 504 | 14.10% | 0.00% | 5.56% | 80.36% | NA |
| Japonica Intermediate | 241 | 64.70% | 0.00% | 0.83% | 34.44% | NA |
| VI/Aromatic | 96 | 75.00% | 0.00% | 2.08% | 22.92% | NA |
| Intermediate | 90 | 37.80% | 0.00% | 3.33% | 58.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725421377 | A -> DEL | LOC_Os07g42460.1 | N | frameshift_variant | Average:7.82; most accessible tissue: Zhenshan97 flag leaf, score: 13.342 | N | N | N | N |
| vg0725421377 | A -> C | LOC_Os07g42460.1 | synonymous_variant ; p.Ser11Ser; LOW | synonymous_codon | Average:7.82; most accessible tissue: Zhenshan97 flag leaf, score: 13.342 | N | N | N | N |