| Variant ID: vg1216387320 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16387320 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TACTTTCCCGTAGCCATGGTGCTACCAAATATTGTAAGCATCTCACCATAGTGTGCAAGAGGTTTGTTAAAATAATCAGCATCAGCCTTGTGATCCTTCG[G/A]
TGAAACAAAATTTTTTTAAGTAAATGCAATAAAACAAATGAATGGAATAAAGCACTAGGTCAAGACATTTACCTCAATATAGCCATTGTAGTGCTCATCA
TGATGAGCACTACAATGGCTATATTGAGGTAAATGTCTTGACCTAGTGCTTTATTCCATTCATTTGTTTTATTGCATTTACTTAAAAAAATTTTGTTTCA[C/T]
CGAAGGATCACAAGGCTGATGCTGATTATTTTAACAAACCTCTTGCACACTATGGTGAGATGCTTACAATATTTGGTAGCACCATGGCTACGGGAAAGTA
| 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 | 68.30% | 0.40% | 19.00% | 12.27% | NA |
| All Indica | 2759 | 57.30% | 0.60% | 27.26% | 14.79% | NA |
| All Japonica | 1512 | 81.80% | 0.00% | 7.80% | 10.38% | NA |
| Aus | 269 | 93.70% | 0.40% | 2.60% | 3.35% | NA |
| Indica I | 595 | 43.40% | 0.00% | 47.90% | 8.74% | NA |
| Indica II | 465 | 56.10% | 0.90% | 24.52% | 18.49% | NA |
| Indica III | 913 | 66.90% | 0.90% | 14.68% | 17.52% | NA |
| Indica Intermediate | 786 | 57.50% | 0.60% | 27.86% | 13.99% | NA |
| Temperate Japonica | 767 | 90.20% | 0.00% | 4.43% | 5.35% | NA |
| Tropical Japonica | 504 | 69.00% | 0.00% | 12.70% | 18.25% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 8.30% | 9.96% | NA |
| VI/Aromatic | 96 | 92.70% | 1.00% | 5.21% | 1.04% | NA |
| Intermediate | 90 | 76.70% | 0.00% | 17.78% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216387320 | G -> DEL | N | N | silent_mutation | Average:5.159; most accessible tissue: Callus, score: 10.072 | N | N | N | N |
| vg1216387320 | G -> A | LOC_Os12g27800.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:5.159; most accessible tissue: Callus, score: 10.072 | N | N | N | N |
| vg1216387320 | G -> A | LOC_Os12g27810.1 | upstream_gene_variant ; 4105.0bp to feature; MODIFIER | silent_mutation | Average:5.159; most accessible tissue: Callus, score: 10.072 | N | N | N | N |
| vg1216387320 | G -> A | LOC_Os12g27790.1 | downstream_gene_variant ; 3298.0bp to feature; MODIFIER | silent_mutation | Average:5.159; most accessible tissue: Callus, score: 10.072 | N | N | N | N |