| Variant ID: vg0221509991 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21509991 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CGGCCGCCCCCGGGTCCGCCGCTCGGTCAGGGCGGCGGGACAGGAGGAGGAAGAAGAGGTCGGCCCATTCCGACGACGAGGGTCATGTCCTCGCCGTCGA[A/G]
GGCGTTTCGCTGGCCACCCGAAAGGGGAGGCCTGCGAGCGACAAAAAGAAGGAAGCCGACACTCCCTGACCTCGGCTACTTGGAAGAGCGAAGGCGGCGC
GCGCCGCCTTCGCTCTTCCAAGTAGCCGAGGTCAGGGAGTGTCGGCTTCCTTCTTTTTGTCGCTCGCAGGCCTCCCCTTTCGGGTGGCCAGCGAAACGCC[T/C]
TCGACGGCGAGGACATGACCCTCGTCGTCGGAATGGGCCGACCTCTTCTTCCTCCTCCTGTCCCGCCGCCCTGACCGAGCGGCGGACCCGGGGGCGGCCG
| 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 | 40.20% | 0.20% | 6.54% | 53.05% | NA |
| All Indica | 2759 | 4.90% | 0.30% | 7.68% | 87.06% | NA |
| All Japonica | 1512 | 98.00% | 0.00% | 0.93% | 1.06% | NA |
| Aus | 269 | 47.20% | 0.00% | 27.14% | 25.65% | NA |
| Indica I | 595 | 4.20% | 0.00% | 11.60% | 84.20% | NA |
| Indica II | 465 | 5.40% | 0.00% | 8.39% | 86.24% | NA |
| Indica III | 913 | 3.70% | 1.00% | 2.63% | 92.66% | NA |
| Indica Intermediate | 786 | 6.60% | 0.00% | 10.18% | 83.21% | NA |
| Temperate Japonica | 767 | 99.10% | 0.00% | 0.52% | 0.39% | NA |
| Tropical Japonica | 504 | 96.00% | 0.00% | 1.59% | 2.38% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.83% | 0.41% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 68.90% | 0.00% | 8.89% | 22.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221509991 | A -> G | LOC_Os02g35780.1 | downstream_gene_variant ; 4502.0bp to feature; MODIFIER | silent_mutation | Average:6.528; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg0221509991 | A -> G | LOC_Os02g35790.1 | downstream_gene_variant ; 2482.0bp to feature; MODIFIER | silent_mutation | Average:6.528; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg0221509991 | A -> G | LOC_Os02g35810.1 | downstream_gene_variant ; 3041.0bp to feature; MODIFIER | silent_mutation | Average:6.528; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg0221509991 | A -> G | LOC_Os02g35800.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.528; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg0221509991 | A -> DEL | N | N | silent_mutation | Average:6.528; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |