| Variant ID: vg0131450301 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31450301 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTCCTGTGGATGTCGAAGTCGCGGATCCTTCGGCCCTCTCAAGTGCCTTCTCCCGCCTAGGACTTTGGCGTGGAGGTGGCGGTGGAGTACGAGCTCGACG[A/G]
CGTGGGTTTGGCTCCCCGTCGTCACCGCTCATACTCGGGGAGAGGTCGTGCGCCTTTGCTGGCTCGGCCATTGGGCTGAACAGGAAAAGCTTGGCGCACA
TGTGCGCCAAGCTTTTCCTGTTCAGCCCAATGGCCGAGCCAGCAAAGGCGCACGACCTCTCCCCGAGTATGAGCGGTGACGACGGGGAGCCAAACCCACG[T/C]
CGTCGAGCTCGTACTCCACCGCCACCTCCACGCCAAAGTCCTAGGCGGGAGAAGGCACTTGAGAGGGCCGAAGGATCCGCGACTTCGACATCCACAGGAG
| 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 | 16.00% | 15.40% | 3.94% | 64.62% | NA |
| All Indica | 2759 | 2.20% | 0.50% | 6.52% | 90.79% | NA |
| All Japonica | 1512 | 43.90% | 39.10% | 0.20% | 16.80% | NA |
| Aus | 269 | 0.00% | 0.70% | 0.37% | 98.88% | NA |
| Indica I | 595 | 3.90% | 0.00% | 7.23% | 88.91% | NA |
| Indica II | 465 | 1.10% | 0.20% | 8.17% | 90.54% | NA |
| Indica III | 913 | 0.30% | 0.40% | 4.16% | 95.07% | NA |
| Indica Intermediate | 786 | 3.80% | 1.00% | 7.76% | 87.40% | NA |
| Temperate Japonica | 767 | 71.30% | 16.40% | 0.00% | 12.26% | NA |
| Tropical Japonica | 504 | 6.30% | 83.50% | 0.40% | 9.72% | NA |
| Japonica Intermediate | 241 | 35.30% | 18.30% | 0.41% | 46.06% | NA |
| VI/Aromatic | 96 | 5.20% | 90.60% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 30.00% | 40.00% | 2.22% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131450301 | A -> G | LOC_Os01g54660.1 | synonymous_variant ; p.Arg24Arg; LOW | synonymous_codon | Average:34.292; most accessible tissue: Zhenshan97 panicle, score: 75.67 | N | N | N | N |
| vg0131450301 | A -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:34.292; most accessible tissue: Zhenshan97 panicle, score: 75.67 | N | N | N | N |