| Variant ID: vg1218481397 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481397 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CGGTCAGCGCCGCCACTTCCCTCGGCTCCGCAAAGTCGAGCTCTACCCCGGCCACCCGTTCTTTTGCGCTGAACCCCGCCGGAAGTCGCCGTCACCGTGA[A/G]
GGCCGAACCGTTGCCATGTTTTGATCTCCAACGAAGCTTTGCCGTCGACTCCGTGGTCGCCGGACCTCGCCGTATCCACTGTCGGCATCGCAGCAGTGAG
CTCACTGCTGCGATGCCGACAGTGGATACGGCGAGGTCCGGCGACCACGGAGTCGACGGCAAAGCTTCGTTGGAGATCAAAACATGGCAACGGTTCGGCC[T/C]
TCACGGTGACGGCGACTTCCGGCGGGGTTCAGCGCAAAAGAACGGGTGGCCGGGGTAGAGCTCGACTTTGCGGAGCCGAGGGAAGTGGCGGCGCTGACCG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 13.10% | 0.30% | 2.79% | 83.75% | NA |
| All Indica | 2759 | 2.20% | 0.50% | 3.04% | 94.20% | NA |
| All Japonica | 1512 | 35.10% | 0.00% | 0.46% | 64.48% | NA |
| Aus | 269 | 1.50% | 0.00% | 13.75% | 84.76% | NA |
| Indica I | 595 | 3.50% | 0.00% | 1.85% | 94.62% | NA |
| Indica II | 465 | 3.00% | 0.00% | 2.80% | 94.19% | NA |
| Indica III | 913 | 0.30% | 1.60% | 3.07% | 94.96% | NA |
| Indica Intermediate | 786 | 2.90% | 0.00% | 4.07% | 93.00% | NA |
| Temperate Japonica | 767 | 59.60% | 0.00% | 0.39% | 40.03% | NA |
| Tropical Japonica | 504 | 3.00% | 0.00% | 0.40% | 96.63% | NA |
| Japonica Intermediate | 241 | 24.10% | 0.00% | 0.83% | 75.10% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 1.04% | 98.96% | NA |
| Intermediate | 90 | 27.80% | 1.10% | 3.33% | 67.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481397 | A -> DEL | LOC_Os12g30780.1 | N | frameshift_variant | Average:23.468; most accessible tissue: Minghui63 young leaf, score: 38.036 | N | N | N | N |
| vg1218481397 | A -> G | LOC_Os12g30780.1 | missense_variant ; p.Leu47Pro; MODERATE | nonsynonymous_codon ; L47P | Average:23.468; most accessible tissue: Minghui63 young leaf, score: 38.036 | unknown | unknown | DELETERIOUS | 0.02 |