| Variant ID: vg0233325660 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 33325660 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCCGTCGTCGGCCCGCACGAGCTCATCATGAGCGCCTGCAGCTCGAACTCCTTGGGGTAGACGAAGAGGTAGATGAACCCGAGGAGCAGCAGCGGCAGCA[G/A]
CACCAGCGCCTTGCTTGACGCCGACAGCTTGGGGAAGCCATGCTTAGAGCTCTTCGCCGGCGGCATGGCAGGCAAGAGCTCGAGCTCGACACAGTCGTCG
CGACGACTGTGTCGAGCTCGAGCTCTTGCCTGCCATGCCGCCGGCGAAGAGCTCTAAGCATGGCTTCCCCAAGCTGTCGGCGTCAAGCAAGGCGCTGGTG[C/T]
TGCTGCCGCTGCTGCTCCTCGGGTTCATCTACCTCTTCGTCTACCCCAAGGAGTTCGAGCTGCAGGCGCTCATGATGAGCTCGTGCGGGCCGACGACGGC
| 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 | 98.10% | 1.40% | 0.51% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 94.20% | 4.20% | 1.52% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 91.10% | 6.30% | 2.61% | 0.00% | NA |
| Tropical Japonica | 504 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 96.30% | 2.50% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 2.20% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0233325660 | G -> A | LOC_Os02g54370.1 | synonymous_variant ; p.Leu89Leu; LOW | synonymous_codon | Average:61.786; most accessible tissue: Zhenshan97 root, score: 74.466 | N | N | N | N |