| Variant ID: vg0221510713 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21510713 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGCTGATGCGCGCGATTTGCGACCGCCGGGATTCTGCCCGAAGAGAGAGAGAGCAGGGAGGAGAGGCCCCCGAGCCGAACGGCGGCCTAAGGCCCCCGAC[G/A]
ACCGGAGCTGGCCCTCCGCCTGCTTGTCCGACGGTGCCAGGCGCCCCCGACCCCCAGGATGGCCCCGAGGCCACTGCGGGAAGGCCGCGCCTGTCGCCCT
AGGGCGACAGGCGCGGCCTTCCCGCAGTGGCCTCGGGGCCATCCTGGGGGTCGGGGGCGCCTGGCACCGTCGGACAAGCAGGCGGAGGGCCAGCTCCGGT[C/T]
GTCGGGGGCCTTAGGCCGCCGTTCGGCTCGGGGGCCTCTCCTCCCTGCTCTCTCTCTCTTCGGGCAGAATCCCGGCGGTCGCAAATCGCGCGCATCAGCA
| 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 | 35.80% | 0.20% | 3.72% | 60.28% | NA |
| All Indica | 2759 | 4.70% | 0.00% | 4.39% | 90.87% | NA |
| All Japonica | 1512 | 93.80% | 0.70% | 2.18% | 3.31% | NA |
| Aus | 269 | 0.70% | 0.00% | 6.32% | 92.94% | NA |
| Indica I | 595 | 2.40% | 0.00% | 5.04% | 92.61% | NA |
| Indica II | 465 | 3.90% | 0.00% | 2.80% | 93.33% | NA |
| Indica III | 913 | 6.70% | 0.00% | 4.05% | 89.27% | NA |
| Indica Intermediate | 786 | 4.80% | 0.00% | 5.22% | 89.95% | NA |
| Temperate Japonica | 767 | 93.40% | 1.30% | 4.17% | 1.17% | NA |
| Tropical Japonica | 504 | 93.10% | 0.00% | 0.20% | 6.75% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 2.08% | 7.29% | NA |
| Intermediate | 90 | 57.80% | 0.00% | 3.33% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221510713 | G -> A | LOC_Os02g35800.1 | synonymous_variant ; p.Thr575Thr; LOW | synonymous_codon | Average:13.877; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0221510713 | G -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:13.877; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |