| Variant ID: vg0221509995 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21509995 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGCCCCCGGGTCCGCCGCTCGGTCAGGGCGGCGGGACAGGAGGAGGAAGAAGAGGTCGGCCCATTCCGACGACGAGGGTCATGTCCTCGCCGTCGAAGGC[G/A]
TTTCGCTGGCCACCCGAAAGGGGAGGCCTGCGAGCGACAAAAAGAAGGAAGCCGACACTCCCTGACCTCGGCTACTTGGAAGAGCGAAGGCGGCGCGCGG
CCGCGCGCCGCCTTCGCTCTTCCAAGTAGCCGAGGTCAGGGAGTGTCGGCTTCCTTCTTTTTGTCGCTCGCAGGCCTCCCCTTTCGGGTGGCCAGCGAAA[C/T]
GCCTTCGACGGCGAGGACATGACCCTCGTCGTCGGAATGGGCCGACCTCTTCTTCCTCCTCCTGTCCCGCCGCCCTGACCGAGCGGCGGACCCGGGGGCG
| 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 | 41.00% | 0.60% | 6.73% | 51.67% | NA |
| All Indica | 2759 | 7.40% | 0.00% | 7.79% | 84.74% | NA |
| All Japonica | 1512 | 97.20% | 0.40% | 1.32% | 1.06% | NA |
| Aus | 269 | 47.20% | 0.00% | 27.14% | 25.65% | NA |
| Indica I | 595 | 7.90% | 0.00% | 11.93% | 80.17% | NA |
| Indica II | 465 | 5.80% | 0.00% | 9.46% | 84.73% | NA |
| Indica III | 913 | 6.50% | 0.10% | 2.30% | 91.13% | NA |
| Indica Intermediate | 786 | 9.20% | 0.00% | 10.05% | 80.79% | NA |
| Temperate Japonica | 767 | 99.00% | 0.00% | 0.65% | 0.39% | NA |
| Tropical Japonica | 504 | 96.00% | 0.20% | 1.39% | 2.38% | NA |
| Japonica Intermediate | 241 | 94.20% | 2.10% | 3.32% | 0.41% | NA |
| VI/Aromatic | 96 | 79.20% | 19.80% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 68.90% | 0.00% | 10.00% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221509995 | G -> A | LOC_Os02g35780.1 | downstream_gene_variant ; 4506.0bp to feature; MODIFIER | silent_mutation | Average:6.528; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg0221509995 | G -> A | LOC_Os02g35790.1 | downstream_gene_variant ; 2486.0bp to feature; MODIFIER | silent_mutation | Average:6.528; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg0221509995 | G -> A | LOC_Os02g35810.1 | downstream_gene_variant ; 3037.0bp to feature; MODIFIER | silent_mutation | Average:6.528; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg0221509995 | G -> A | LOC_Os02g35800.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.528; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg0221509995 | G -> DEL | N | N | silent_mutation | Average:6.528; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |