| Variant ID: vg0209333926 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9333926 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGGTACACCAAAAGTTGATACAATTCAGAGTTTAACAAGCGGAAGCGTAAATAGTTATTTATTACATGGGCAGCGACGGCCCAGCACACTCAAAGACAAC[G/A]
AAAAACAGCAGAAGACTAAGGCGACGACCACAGGCGCTTGACGGCAGGCACGAGCTAGACACCAAAGCCTTCATCCTCCAGGGGCTCCTCTGCTGGGTTT
AAACCCAGCAGAGGAGCCCCTGGAGGATGAAGGCTTTGGTGTCTAGCTCGTGCCTGCCGTCAAGCGCCTGTGGTCGTCGCCTTAGTCTTCTGCTGTTTTT[C/T]
GTTGTCTTTGAGTGTGCTGGGCCGTCGCTGCCCATGTAATAAATAACTATTTACGCTTCCGCTTGTTAAACTCTGAATTGTATCAACTTTTGGTGTACCT
| 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 | 41.60% | 1.60% | 7.70% | 49.07% | NA |
| All Indica | 2759 | 11.60% | 2.80% | 12.47% | 73.14% | NA |
| All Japonica | 1512 | 97.20% | 0.00% | 0.07% | 2.71% | NA |
| Aus | 269 | 13.00% | 0.00% | 5.95% | 81.04% | NA |
| Indica I | 595 | 23.20% | 0.20% | 4.71% | 71.93% | NA |
| Indica II | 465 | 11.40% | 3.40% | 14.84% | 70.32% | NA |
| Indica III | 913 | 4.30% | 4.10% | 16.76% | 74.92% | NA |
| Indica Intermediate | 786 | 11.50% | 2.90% | 11.96% | 73.66% | NA |
| Temperate Japonica | 767 | 98.00% | 0.00% | 0.13% | 1.83% | NA |
| Tropical Japonica | 504 | 96.00% | 0.00% | 0.00% | 3.97% | 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 | 63.30% | 0.00% | 3.33% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0209333926 | G -> A | LOC_Os02g16390.1 | upstream_gene_variant ; 1904.0bp to feature; MODIFIER | silent_mutation | Average:4.363; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0209333926 | 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 |
| vg0209333926 | G -> DEL | N | N | silent_mutation | Average:4.363; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |