| Variant ID: vg1216602480 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16602480 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGTGTTGTTTCACCTTATATAAAAACAATGTTTCTGCAAGTAGTGAAAGAATATTTCAGTTCAGTGCAATATTAGATCTATACATAGTGAAACATTATAA[G/A]
TACACTAGTTGAAACATTTTTCCGTGGAACAAAAAATGAAACGAATTCCCTTAATAGAGGGTTTCCAAAATATACGGGTGATTTTGTTGCAAAAGAATAT
ATATTCTTTTGCAACAAAATCACCCGTATATTTTGGAAACCCTCTATTAAGGGAATTCGTTTCATTTTTTGTTCCACGGAAAAATGTTTCAACTAGTGTA[C/T]
TTATAATGTTTCACTATGTATAGATCTAATATTGCACTGAACTGAAATATTCTTTCACTACTTGCAGAAACATTGTTTTTATATAAGGTGAAACAACACC
| 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 | 85.20% | 3.40% | 0.36% | 11.05% | NA |
| All Indica | 2759 | 91.10% | 3.70% | 0.25% | 4.93% | NA |
| All Japonica | 1512 | 81.30% | 3.10% | 0.40% | 15.15% | NA |
| Aus | 269 | 53.50% | 0.40% | 0.00% | 46.10% | NA |
| Indica I | 595 | 96.50% | 3.00% | 0.34% | 0.17% | NA |
| Indica II | 465 | 88.80% | 1.90% | 0.65% | 8.60% | NA |
| Indica III | 913 | 92.00% | 4.50% | 0.00% | 3.50% | NA |
| Indica Intermediate | 786 | 87.40% | 4.30% | 0.25% | 8.02% | NA |
| Temperate Japonica | 767 | 99.60% | 0.10% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 50.00% | 6.70% | 0.79% | 42.46% | NA |
| Japonica Intermediate | 241 | 88.80% | 5.00% | 0.83% | 5.39% | NA |
| VI/Aromatic | 96 | 75.00% | 6.20% | 1.04% | 17.71% | NA |
| Intermediate | 90 | 74.40% | 4.40% | 3.33% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216602480 | G -> DEL | N | N | silent_mutation | Average:13.201; most accessible tissue: Zhenshan97 flower, score: 18.233 | N | N | N | N |
| vg1216602480 | G -> A | LOC_Os12g28110.1 | downstream_gene_variant ; 3562.0bp to feature; MODIFIER | silent_mutation | Average:13.201; most accessible tissue: Zhenshan97 flower, score: 18.233 | N | N | N | N |
| vg1216602480 | G -> A | LOC_Os12g28110-LOC_Os12g28137 | intergenic_region ; MODIFIER | silent_mutation | Average:13.201; most accessible tissue: Zhenshan97 flower, score: 18.233 | N | N | N | N |