| Variant ID: vg0221511103 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21511103 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATGCTATCCTGATAACTTCGAGGAAGTTGCGCCATTATTTCCAGGCGCATCGGGTCACGGTGGTTACGTCTTATCCCCTCGGCCAAATCTTGTATAACCG[A/G]
GAGGGTACTGGACGGGTGGTGAAATGGGCAATCGAACTCTCTGAATTCGATTTGCGCTTGAAACCAAGCCACGCGATCAAGAGCCAGGCCCTCGCCGACT
AGTCGGCGAGGGCCTGGCTCTTGATCGCGTGGCTTGGTTTCAAGCGCAAATCGAATTCAGAGAGTTCGATTGCCCATTTCACCACCCGTCCAGTACCCTC[T/C]
CGGTTATACAAGATTTGGCCGAGGGGATAAGACGTAACCACCGTGACCCGATGCGCCTGGAAATAATGGCGCAACTTCCTCGAAGTTATCAGGATAGCAT
| 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 | 35.70% | 0.20% | 1.06% | 63.03% | NA |
| All Indica | 2759 | 2.70% | 0.40% | 1.59% | 95.29% | NA |
| All Japonica | 1512 | 97.00% | 0.00% | 0.07% | 2.98% | NA |
| Aus | 269 | 0.70% | 0.00% | 0.74% | 98.51% | NA |
| Indica I | 595 | 1.80% | 0.00% | 2.02% | 96.13% | NA |
| Indica II | 465 | 3.90% | 0.00% | 1.72% | 94.41% | NA |
| Indica III | 913 | 1.90% | 1.10% | 1.10% | 95.95% | NA |
| Indica Intermediate | 786 | 3.70% | 0.10% | 1.78% | 94.40% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.13% | 0.65% | NA |
| Tropical Japonica | 504 | 93.10% | 0.00% | 0.00% | 6.94% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 61.10% | 0.00% | 3.33% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221511103 | A -> G | LOC_Os02g35800.1 | synonymous_variant ; p.Arg705Arg; LOW | synonymous_codon | Average:6.464; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0221511103 | A -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:6.464; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |