| Variant ID: vg0725421392 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25421392 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GCTTAGGGCTTTGGCGCGGAGGAGGTGGAGGAGTACGAGCTCGACGGCGTGGATTCGGCTCCCCGTCGTCGCCGCTCACACTCGGAGAGAGGTCGTGCGC[T/C]
TTTCCTTGCTCGGCCATTAGGCTGAACAAGAAAAACTTGGCACACACGGAAGAGTCTGAGAGCTCAGAAAACACACGCTGAGCCCCCTACCTGGCGCGCC
GGCGCGCCAGGTAGGGGGCTCAGCGTGTGTTTTCTGAGCTCTCAGACTCTTCCGTGTGTGCCAAGTTTTTCTTGTTCAGCCTAATGGCCGAGCAAGGAAA[A/G]
GCGCACGACCTCTCTCCGAGTGTGAGCGGCGACGACGGGGAGCCGAATCCACGCCGTCGAGCTCGTACTCCTCCACCTCCTCCGCGCCAAAGCCCTAAGC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 23.40% | 0.30% | 1.97% | 74.38% | NA |
| All Indica | 2759 | 3.70% | 0.40% | 2.68% | 93.15% | NA |
| All Japonica | 1512 | 60.20% | 0.00% | 0.26% | 39.55% | NA |
| Aus | 269 | 1.90% | 0.00% | 0.74% | 97.40% | NA |
| Indica I | 595 | 4.50% | 1.50% | 2.18% | 91.76% | NA |
| Indica II | 465 | 3.70% | 0.00% | 0.65% | 95.70% | NA |
| Indica III | 913 | 2.70% | 0.10% | 4.16% | 92.99% | NA |
| Indica Intermediate | 786 | 4.30% | 0.30% | 2.54% | 92.88% | NA |
| Temperate Japonica | 767 | 89.70% | 0.00% | 0.26% | 10.04% | NA |
| Tropical Japonica | 504 | 13.30% | 0.00% | 0.20% | 86.51% | NA |
| Japonica Intermediate | 241 | 64.30% | 0.00% | 0.41% | 35.27% | NA |
| VI/Aromatic | 96 | 62.50% | 0.00% | 4.17% | 33.33% | NA |
| Intermediate | 90 | 31.10% | 0.00% | 10.00% | 58.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725421392 | T -> DEL | LOC_Os07g42460.1 | N | frameshift_variant | Average:7.82; most accessible tissue: Zhenshan97 flag leaf, score: 13.342 | N | N | N | N |
| vg0725421392 | T -> C | LOC_Os07g42460.1 | synonymous_variant ; p.Lys6Lys; LOW | synonymous_codon | Average:7.82; most accessible tissue: Zhenshan97 flag leaf, score: 13.342 | N | N | N | N |