| Variant ID: vg1225601599 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25601599 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCTCCCCCCACCATGCCTTAGGCAGTCCCGCGGTGTCCAACATGGCATTCACCAAGTCAGTCAGTGTGCGGTTCTTCCTTTCAGCAATCCCATTAGACTC[G/A]
GGAGAATAGGGAGGCGTCCTCTCATGTATGATGCCATGTTCCTCACAGAATAAGTCAAACTCGTTCGAGAAAAACTCTCCACCACGATCAGACCTAAGCC
GGCTTAGGTCTGATCGTGGTGGAGAGTTTTTCTCGAACGAGTTTGACTTATTCTGTGAGGAACATGGCATCATACATGAGAGGACGCCTCCCTATTCTCC[C/T]
GAGTCTAATGGGATTGCTGAAAGGAAGAACCGCACACTGACTGACTTGGTGAATGCCATGTTGGACACCGCGGGACTGCCTAAGGCATGGTGGGGGGAGG
| 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 | 55.00% | 1.50% | 11.55% | 31.91% | NA |
| All Indica | 2759 | 42.80% | 0.20% | 13.05% | 43.93% | NA |
| All Japonica | 1512 | 86.00% | 3.90% | 10.05% | 0.07% | NA |
| Aus | 269 | 3.30% | 0.00% | 4.46% | 92.19% | NA |
| Indica I | 595 | 86.70% | 0.00% | 2.69% | 10.59% | NA |
| Indica II | 465 | 18.50% | 0.90% | 13.33% | 67.31% | NA |
| Indica III | 913 | 30.20% | 0.00% | 20.70% | 49.07% | NA |
| Indica Intermediate | 786 | 38.50% | 0.30% | 11.83% | 49.36% | NA |
| Temperate Japonica | 767 | 91.40% | 0.00% | 8.60% | 0.00% | NA |
| Tropical Japonica | 504 | 85.50% | 10.50% | 3.97% | 0.00% | NA |
| Japonica Intermediate | 241 | 69.70% | 2.50% | 27.39% | 0.41% | NA |
| VI/Aromatic | 96 | 61.50% | 0.00% | 12.50% | 26.04% | NA |
| Intermediate | 90 | 57.80% | 6.70% | 11.11% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225601599 | G -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:10.309; most accessible tissue: Zhenshan97 flower, score: 19.853 | N | N | N | N |
| vg1225601599 | G -> A | LOC_Os12g41280.1 | synonymous_variant ; p.Pro588Pro; LOW | synonymous_codon | Average:10.309; most accessible tissue: Zhenshan97 flower, score: 19.853 | N | N | N | N |