| Variant ID: vg1225601251 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25601251 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CAGAGGGTTGGTTCGAACCACTATGTGTATCCTTCATTGGGAAAAAGCTCTCAAAGAAGGTAGCATCACGAGACTCCATAATTGTACCAACATGCATGTC[C/A]
GGTACCTCAGATTTAACTATTGAAAATCTATAGGCAATGCTATGATGAGCATATCCCAGAAAAACACAGTCCACAGTCTTAGGTCCAAGTTTTCGCTTCT
AGAAGCGAAAACTTGGACCTAAGACTGTGGACTGTGTTTTTCTGGGATATGCTCATCATAGCATTGCCTATAGATTTTCAATAGTTAAATCTGAGGTACC[G/T]
GACATGCATGTTGGTACAATTATGGAGTCTCGTGATGCTACCTTCTTTGAGAGCTTTTTCCCAATGAAGGATACACATAGTGGTTCGAACCAACCCTCTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 53.40% | 0.20% | 5.10% | 41.30% | NA |
| All Indica | 2759 | 40.10% | 0.00% | 0.87% | 59.04% | NA |
| All Japonica | 1512 | 86.40% | 0.20% | 13.36% | 0.07% | NA |
| Aus | 269 | 1.10% | 0.40% | 0.74% | 97.77% | NA |
| Indica I | 595 | 86.40% | 0.00% | 0.17% | 13.45% | NA |
| Indica II | 465 | 13.50% | 0.00% | 0.86% | 85.59% | NA |
| Indica III | 913 | 26.40% | 0.00% | 1.20% | 72.40% | NA |
| Indica Intermediate | 786 | 36.50% | 0.10% | 1.02% | 62.34% | NA |
| Temperate Japonica | 767 | 86.30% | 0.30% | 13.43% | 0.00% | NA |
| Tropical Japonica | 504 | 96.00% | 0.00% | 3.97% | 0.00% | NA |
| Japonica Intermediate | 241 | 66.40% | 0.40% | 32.78% | 0.41% | NA |
| VI/Aromatic | 96 | 59.40% | 3.10% | 10.42% | 27.08% | NA |
| Intermediate | 90 | 60.00% | 0.00% | 3.33% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225601251 | C -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:12.951; most accessible tissue: Zhenshan97 flower, score: 23.247 | N | N | N | N |
| vg1225601251 | C -> A | LOC_Os12g41280.1 | synonymous_variant ; p.Pro704Pro; LOW | synonymous_codon | Average:12.951; most accessible tissue: Zhenshan97 flower, score: 23.247 | N | N | N | N |