| Variant ID: vg0209333855 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9333855 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACTTGTCACGACCGGAAATAACCCAACGGGCGTTCCTTACGTGCGTGTATTATTCCTTGTCCCAGGAGGCAAGGTACACCAAAAGTTGATACAATTCAGA[G/A]
TTTAACAAGCGGAAGCGTAAATAGTTATTTATTACATGGGCAGCGACGGCCCAGCACACTCAAAGACAACGAAAAACAGCAGAAGACTAAGGCGACGACC
GGTCGTCGCCTTAGTCTTCTGCTGTTTTTCGTTGTCTTTGAGTGTGCTGGGCCGTCGCTGCCCATGTAATAAATAACTATTTACGCTTCCGCTTGTTAAA[C/T]
TCTGAATTGTATCAACTTTTGGTGTACCTTGCCTCCTGGGACAAGGAATAATACACGCACGTAAGGAACGCCCGTTGGGTTATTTCCGGTCGTGACAAGT
| 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 | 42.50% | 0.10% | 3.39% | 53.96% | NA |
| All Indica | 2759 | 13.20% | 0.00% | 5.18% | 81.62% | NA |
| All Japonica | 1512 | 97.20% | 0.00% | 0.07% | 2.71% | NA |
| Aus | 269 | 13.40% | 1.90% | 5.58% | 79.18% | NA |
| Indica I | 595 | 25.90% | 0.00% | 1.34% | 72.77% | NA |
| Indica II | 465 | 13.80% | 0.00% | 9.89% | 76.34% | NA |
| Indica III | 913 | 3.60% | 0.00% | 3.94% | 92.44% | NA |
| Indica Intermediate | 786 | 14.40% | 0.00% | 6.74% | 78.88% | NA |
| Temperate Japonica | 767 | 98.00% | 0.00% | 0.00% | 1.96% | NA |
| Tropical Japonica | 504 | 96.00% | 0.00% | 0.20% | 3.77% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 0.00% | 12.50% | NA |
| Intermediate | 90 | 62.20% | 1.10% | 1.11% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0209333855 | G -> A | LOC_Os02g16390.1 | upstream_gene_variant ; 1975.0bp to feature; MODIFIER | silent_mutation | Average:4.363; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0209333855 | G -> A | LOC_Os02g16380.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.363; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0209333855 | G -> DEL | N | N | silent_mutation | Average:4.363; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |