| Variant ID: vg0221510356 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21510356 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CGGCGTCCCCCGGCCGGGCTCCGTTCCGCTGGCCACGGGCGATGGCACAGAGCTGCCTAACCCGTGGAACATCGAACACCTTCGTCGCTTCTACCCCTAA[A/G]
GGGGATCGGGTGTCAGGTTTCGGGCTCGGGCCAACCCCGCACCCCCCTCGGGCGTGCAGGGTTGGCCGGGGGCTACCACATATGCATATTCTTATTTCTC
GAGAAATAAGAATATGCATATGTGGTAGCCCCCGGCCAACCCTGCACGCCCGAGGGGGGTGCGGGGTTGGCCCGAGCCCGAAACCTGACACCCGATCCCC[T/C]
TTAGGGGTAGAAGCGACGAAGGTGTTCGATGTTCCACGGGTTAGGCAGCTCTGTGCCATCGCCCGTGGCCAGCGGAACGGAGCCCGGCCGGGGGACGCCG
| 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 | 35.00% | 0.10% | 0.23% | 64.71% | NA |
| All Indica | 2759 | 2.00% | 0.00% | 0.18% | 97.83% | NA |
| All Japonica | 1512 | 96.60% | 0.10% | 0.00% | 3.31% | NA |
| Aus | 269 | 1.10% | 0.00% | 0.37% | 98.51% | NA |
| Indica I | 595 | 1.70% | 0.00% | 0.34% | 97.98% | NA |
| Indica II | 465 | 1.90% | 0.00% | 0.00% | 98.06% | NA |
| Indica III | 913 | 1.50% | 0.00% | 0.22% | 98.25% | NA |
| Indica Intermediate | 786 | 2.80% | 0.00% | 0.13% | 97.07% | NA |
| Temperate Japonica | 767 | 98.70% | 0.00% | 0.00% | 1.30% | NA |
| Tropical Japonica | 504 | 93.30% | 0.00% | 0.00% | 6.75% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.40% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 88.50% | 2.10% | 3.12% | 6.25% | NA |
| Intermediate | 90 | 55.60% | 0.00% | 2.22% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221510356 | A -> G | LOC_Os02g35780.1 | downstream_gene_variant ; 4867.0bp to feature; MODIFIER | silent_mutation | Average:7.969; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |
| vg0221510356 | A -> G | LOC_Os02g35790.1 | downstream_gene_variant ; 2847.0bp to feature; MODIFIER | silent_mutation | Average:7.969; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |
| vg0221510356 | A -> G | LOC_Os02g35810.1 | downstream_gene_variant ; 2676.0bp to feature; MODIFIER | silent_mutation | Average:7.969; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |
| vg0221510356 | A -> G | LOC_Os02g35800.1 | intron_variant ; MODIFIER | silent_mutation | Average:7.969; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |
| vg0221510356 | A -> DEL | N | N | silent_mutation | Average:7.969; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |