| Variant ID: vg0221510031 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21510031 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CAGGAGGAGGAAGAAGAGGTCGGCCCATTCCGACGACGAGGGTCATGTCCTCGCCGTCGAAGGCGTTTCGCTGGCCACCCGAAAGGGGAGGCCTGCGAGC[G/A]
ACAAAAAGAAGGAAGCCGACACTCCCTGACCTCGGCTACTTGGAAGAGCGAAGGCGGCGCGCGGCCCTTCGAGCCGCGCGCTACCAGCAGAGCCTGCGGC
GCCGCAGGCTCTGCTGGTAGCGCGCGGCTCGAAGGGCCGCGCGCCGCCTTCGCTCTTCCAAGTAGCCGAGGTCAGGGAGTGTCGGCTTCCTTCTTTTTGT[C/T]
GCTCGCAGGCCTCCCCTTTCGGGTGGCCAGCGAAACGCCTTCGACGGCGAGGACATGACCCTCGTCGTCGGAATGGGCCGACCTCTTCTTCCTCCTCCTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.60% | 0.20% | 7.77% | 52.41% | NA |
| All Indica | 2759 | 4.30% | 0.20% | 9.10% | 86.37% | NA |
| All Japonica | 1512 | 97.70% | 0.20% | 1.19% | 0.93% | NA |
| Aus | 269 | 47.60% | 0.00% | 29.74% | 22.68% | NA |
| Indica I | 595 | 3.90% | 0.00% | 14.79% | 81.34% | NA |
| Indica II | 465 | 3.00% | 0.60% | 9.46% | 86.88% | NA |
| Indica III | 913 | 3.90% | 0.00% | 3.18% | 92.88% | NA |
| Indica Intermediate | 786 | 6.00% | 0.30% | 11.45% | 82.32% | NA |
| Temperate Japonica | 767 | 98.70% | 0.30% | 0.65% | 0.39% | NA |
| Tropical Japonica | 504 | 96.00% | 0.00% | 1.79% | 2.18% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.40% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 2.08% | 1.04% | NA |
| Intermediate | 90 | 60.00% | 2.20% | 17.78% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221510031 | G -> A | LOC_Os02g35800.1 | synonymous_variant ; p.Ala434Ala; LOW | synonymous_codon | Average:6.528; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg0221510031 | G -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:6.528; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |