| Variant ID: vg0725421218 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25421218 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GGTCATGGACGACAGGCGGGTGTCGTAGGAGCGCGCCAGCAGCCTGAAGCGCACCCTGAGGCGTGCTGCCGTCGCCGTAGACGAGGAGGCGACGCTCCCC[A/G]
TCTCGCCGTTCTCCTGCATCACCTGCGACTGGTGATGCCACGGATTTGTCGACCCTCTGAAGCGCCTCCCCCTGCTTAGGGCTTTGGCGCGGAGGAGGTG
CACCTCCTCCGCGCCAAAGCCCTAAGCAGGGGGAGGCGCTTCAGAGGGTCGACAAATCCGTGGCATCACCAGTCGCAGGTGATGCAGGAGAACGGCGAGA[T/C]
GGGGAGCGTCGCCTCCTCGTCTACGGCGACGGCAGCACGCCTCAGGGTGCGCTTCAGGCTGCTGGCGCGCTCCTACGACACCCGCCTGTCGTCCATGACC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 24.20% | 0.60% | 1.84% | 73.36% | NA |
| All Indica | 2759 | 5.30% | 0.10% | 1.63% | 92.97% | NA |
| All Japonica | 1512 | 60.30% | 1.60% | 0.93% | 37.17% | NA |
| Aus | 269 | 1.90% | 0.00% | 1.49% | 96.65% | NA |
| Indica I | 595 | 4.90% | 0.00% | 1.18% | 93.95% | NA |
| Indica II | 465 | 2.80% | 0.20% | 1.29% | 95.70% | NA |
| Indica III | 913 | 7.00% | 0.00% | 2.08% | 90.91% | NA |
| Indica Intermediate | 786 | 5.20% | 0.10% | 1.65% | 93.00% | NA |
| Temperate Japonica | 767 | 89.40% | 0.00% | 0.13% | 10.43% | NA |
| Tropical Japonica | 504 | 15.30% | 4.80% | 1.59% | 78.37% | NA |
| Japonica Intermediate | 241 | 61.80% | 0.00% | 2.07% | 36.10% | NA |
| VI/Aromatic | 96 | 54.20% | 0.00% | 17.71% | 28.12% | NA |
| Intermediate | 90 | 32.20% | 1.10% | 7.78% | 58.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725421218 | A -> DEL | LOC_Os07g42460.1 | N | frameshift_variant | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0725421218 | A -> G | LOC_Os07g42460.1 | synonymous_variant ; p.Asp64Asp; LOW | synonymous_codon | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |