| Variant ID: vg1216387273 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16387273 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CAGTTTGGACATCCTCTGTTCCTAGGACTGAATTTGAGTCCTTTGCATACTTTCCCGTAGCCATGGTGCTACCAAATATTGTAAGCATCTCACCATAGTG[T/C]
GCAAGAGGTTTGTTAAAATAATCAGCATCAGCCTTGTGATCCTTCGGTGAAACAAAATTTTTTTAAGTAAATGCAATAAAACAAATGAATGGAATAAAGC
GCTTTATTCCATTCATTTGTTTTATTGCATTTACTTAAAAAAATTTTGTTTCACCGAAGGATCACAAGGCTGATGCTGATTATTTTAACAAACCTCTTGC[A/G]
CACTATGGTGAGATGCTTACAATATTTGGTAGCACCATGGCTACGGGAAAGTATGCAAAGGACTCAAATTCAGTCCTAGGAACAGAGGATGTCCAAACTG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 74.50% | 0.00% | 14.68% | 10.73% | NA |
| All Indica | 2759 | 65.60% | 0.10% | 20.84% | 13.48% | NA |
| All Japonica | 1512 | 85.50% | 0.00% | 6.55% | 7.94% | NA |
| Aus | 269 | 95.20% | 0.00% | 1.49% | 3.35% | NA |
| Indica I | 595 | 52.30% | 0.00% | 39.83% | 7.90% | NA |
| Indica II | 465 | 60.90% | 0.00% | 21.29% | 17.85% | NA |
| Indica III | 913 | 77.80% | 0.00% | 7.12% | 15.12% | NA |
| Indica Intermediate | 786 | 64.40% | 0.30% | 22.14% | 13.23% | NA |
| Temperate Japonica | 767 | 94.30% | 0.00% | 3.78% | 1.96% | NA |
| Tropical Japonica | 504 | 71.80% | 0.00% | 10.71% | 17.46% | NA |
| Japonica Intermediate | 241 | 86.30% | 0.00% | 6.64% | 7.05% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 77.80% | 0.00% | 16.67% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216387273 | T -> C | LOC_Os12g27800.1 | synonymous_variant ; p.Ala425Ala; LOW | synonymous_codon | Average:5.247; most accessible tissue: Callus, score: 10.072 | N | N | N | N |
| vg1216387273 | T -> C | LOC_Os12g27800.1 | synonymous_variant ; p.Ala425Ala; LOW | nonsynonymous_codon ; A425V | Average:5.247; most accessible tissue: Callus, score: 10.072 | unknown | unknown | TOLERATED | 0.26 |
| vg1216387273 | T -> DEL | LOC_Os12g27800.1 | N | frameshift_variant | Average:5.247; most accessible tissue: Callus, score: 10.072 | N | N | N | N |