| Variant ID: vg1201715730 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 1715730 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGCCGTGTAACCACTCCTTCCACGAGATCTGCCTCTTCCGTTGGCTCAGCGAAAGCTGCCTCTGTCCTCTCTGCCGCTACGCGCTGCCCAAGCAGCAGCA[G/A]
GTTCAAAGCTGCTGATGATGCTATTTATGTTTCGGTTCACCAACAGATCCGTTTGTAACTTGTAAGCATATTGCCATCGATATAGAAGTAGAATCATGTT
AACATGATTCTACTTCTATATCGATGGCAATATGCTTACAAGTTACAAACGGATCTGTTGGTGAACCGAAACATAAATAGCATCATCAGCAGCTTTGAAC[C/T]
TGCTGCTGCTTGGGCAGCGCGTAGCGGCAGAGAGGACAGAGGCAGCTTTCGCTGAGCCAACGGAAGAGGCAGATCTCGTGGAAGGAGTGGTTACACGGCA
| 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 | 44.40% | 0.30% | 2.18% | 53.17% | NA |
| All Indica | 2759 | 9.10% | 0.40% | 3.48% | 87.02% | NA |
| All Japonica | 1512 | 97.20% | 0.00% | 0.00% | 2.78% | NA |
| Aus | 269 | 82.90% | 0.00% | 2.60% | 14.50% | NA |
| Indica I | 595 | 3.00% | 0.00% | 4.20% | 92.77% | NA |
| Indica II | 465 | 5.40% | 0.00% | 2.37% | 92.26% | NA |
| Indica III | 913 | 11.20% | 0.20% | 4.05% | 84.56% | NA |
| Indica Intermediate | 786 | 13.40% | 1.30% | 2.93% | 82.44% | NA |
| Temperate Japonica | 767 | 95.60% | 0.00% | 0.00% | 4.43% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 68.90% | 0.00% | 0.00% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1201715730 | G -> DEL | LOC_Os12g04090.1 | N | frameshift_variant | Average:13.021; most accessible tissue: Callus, score: 87.737 | N | N | N | N |
| vg1201715730 | G -> A | LOC_Os12g04090.1 | synonymous_variant ; p.Gln185Gln; LOW | synonymous_codon | Average:13.021; most accessible tissue: Callus, score: 87.737 | N | N | N | N |