| Variant ID: vg0313175610 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 13175610 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GGGGTGACACAACTGAACAAGTTGGAGGACCTAAACGAGTGATCTGCAAGTTTAGGGACCGGGATGACACAGTCAAACAAGTTTGAGGACCTGAACGGTC[A/G]
ATTTGCGAGTTTAGAGACCGGGATGACACAGCGATACAAGTTTAGAGACCGGTGATAGATTTACTCTTTTTTTTTAAACTCATGCATTTAATTAAAGTTC
GAACTTTAATTAAATGCATGAGTTTAAAAAAAAAGAGTAAATCTATCACCGGTCTCTAAACTTGTATCGCTGTGTCATCCCGGTCTCTAAACTCGCAAAT[T/C]
GACCGTTCAGGTCCTCAAACTTGTTTGACTGTGTCATCCCGGTCCCTAAACTTGCAGATCACTCGTTTAGGTCCTCCAACTTGTTCAGTTGTGTCACCCC
| 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 | 22.60% | 1.30% | 6.67% | 69.36% | NA |
| All Indica | 2759 | 1.40% | 2.10% | 6.78% | 89.74% | NA |
| All Japonica | 1512 | 62.40% | 0.00% | 0.20% | 37.37% | NA |
| Aus | 269 | 26.40% | 2.20% | 44.61% | 26.77% | NA |
| Indica I | 595 | 0.70% | 0.30% | 3.87% | 95.13% | NA |
| Indica II | 465 | 0.20% | 0.40% | 0.65% | 98.71% | NA |
| Indica III | 913 | 1.50% | 4.20% | 11.17% | 83.13% | NA |
| Indica Intermediate | 786 | 2.50% | 1.90% | 7.51% | 88.04% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 0.13% | 3.39% | NA |
| Tropical Japonica | 504 | 17.70% | 0.00% | 0.40% | 81.94% | NA |
| Japonica Intermediate | 241 | 47.70% | 0.00% | 0.00% | 52.28% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 1.04% | 97.92% | NA |
| Intermediate | 90 | 16.70% | 0.00% | 4.44% | 78.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0313175610 | A -> DEL | N | N | silent_mutation | Average:54.68; most accessible tissue: Minghui63 panicle, score: 78.92 | N | N | N | N |
| vg0313175610 | A -> G | LOC_Os03g22810.1 | upstream_gene_variant ; 3560.0bp to feature; MODIFIER | silent_mutation | Average:54.68; most accessible tissue: Minghui63 panicle, score: 78.92 | N | N | N | N |
| vg0313175610 | A -> G | LOC_Os03g22800-LOC_Os03g22810 | intergenic_region ; MODIFIER | silent_mutation | Average:54.68; most accessible tissue: Minghui63 panicle, score: 78.92 | N | N | N | N |