| Variant ID: vg1218480675 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18480675 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGCAACAACCATTGTTCTGCCATCCCCTGGTCGCAAGCCGGTCTAAAGTCCAGACTCTGTTCTGAATGATGAGCCAAGCATGAAATTTGCATTTCCCCGG[C/T]
GCCCAGGGTTTCCAAATCAAGGAATTGAAGTTTGTACTCGGCGCCCCGCAGCACTGCGCATGGTAAGCCGAGGAGGCCGTGTAGTGCCCGTTGTTTGTGA
TCACAAACAACGGGCACTACACGGCCTCCTCGGCTTACCATGCGCAGTGCTGCGGGGCGCCGAGTACAAACTTCAATTCCTTGATTTGGAAACCCTGGGC[G/A]
CCGGGGAAATGCAAATTTCATGCTTGGCTCATCATTCAGAACAGAGTCTGGACTTTAGACCGGCTTGCGACCAGGGGATGGCAGAACAATGGTTGTTGCC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 13.20% | 0.20% | 4.66% | 81.93% | NA |
| All Indica | 2759 | 2.60% | 0.00% | 3.37% | 94.02% | NA |
| All Japonica | 1512 | 34.60% | 0.50% | 0.40% | 64.48% | NA |
| Aus | 269 | 1.90% | 0.00% | 42.01% | 56.13% | NA |
| Indica I | 595 | 2.90% | 0.00% | 0.34% | 96.81% | NA |
| Indica II | 465 | 4.70% | 0.00% | 2.80% | 92.47% | NA |
| Indica III | 913 | 0.70% | 0.00% | 4.38% | 94.96% | NA |
| Indica Intermediate | 786 | 3.40% | 0.00% | 4.83% | 91.73% | NA |
| Temperate Japonica | 767 | 60.00% | 0.00% | 0.39% | 39.63% | NA |
| Tropical Japonica | 504 | 2.80% | 0.20% | 0.60% | 96.43% | NA |
| Japonica Intermediate | 241 | 20.30% | 2.90% | 0.00% | 76.76% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 3.12% | 96.88% | NA |
| Intermediate | 90 | 28.90% | 0.00% | 5.56% | 65.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218480675 | C -> DEL | LOC_Os12g30780.1 | N | frameshift_variant | Average:7.299; most accessible tissue: Callus, score: 17.876 | N | N | N | N |
| vg1218480675 | C -> T | LOC_Os12g30780.1 | synonymous_variant ; p.Ala112Ala; LOW | synonymous_codon | Average:7.299; most accessible tissue: Callus, score: 17.876 | N | N | N | N |