| Variant ID: vg0221509088 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21509088 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TGGCCAACTTGGTCATGACGGCACGGCAGCGCCTAGGTGCTGGTGGGCGGTCCTCCGCCACCAAGACCTCTGGCGCTACTACCACCGGCTCCGTGTCGTC[A/G]
AGGCGGAGGGCGCGGCGAGCGGCGGCTGTTGCTCGCCATTCGGCCGCCACTCCTTCGTCAGCGCCTCCGACCCAGGAAGATCTGCGTGGGGGGCCGGATG
CATCCGGCCCCCCACGCAGATCTTCCTGGGTCGGAGGCGCTGACGAAGGAGTGGCGGCCGAATGGCGAGCAACAGCCGCCGCTCGCCGCGCCCTCCGCCT[T/C]
GACGACACGGAGCCGGTGGTAGTAGCGCCAGAGGTCTTGGTGGCGGAGGACCGCCCACCAGCACCTAGGCGCTGCCGTGCCGTCATGACCAAGTTGGCCA
| 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 | 35.20% | 0.10% | 0.55% | 64.13% | NA |
| All Indica | 2759 | 2.40% | 0.20% | 0.72% | 96.74% | NA |
| All Japonica | 1512 | 96.50% | 0.00% | 0.00% | 3.51% | NA |
| Aus | 269 | 0.70% | 0.00% | 0.00% | 99.26% | NA |
| Indica I | 595 | 2.00% | 0.00% | 0.34% | 97.65% | NA |
| Indica II | 465 | 2.40% | 0.90% | 0.65% | 96.13% | NA |
| Indica III | 913 | 1.60% | 0.00% | 1.10% | 97.26% | NA |
| Indica Intermediate | 786 | 3.40% | 0.10% | 0.64% | 95.80% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 93.10% | 0.00% | 0.00% | 6.94% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 1.04% | 8.33% | NA |
| Intermediate | 90 | 56.70% | 0.00% | 5.56% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221509088 | A -> G | LOC_Os02g35800.1 | synonymous_variant ; p.Ser142Ser; LOW | synonymous_codon | Average:8.891; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0221509088 | A -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:8.891; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |