| Variant ID: vg1216387459 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16387459 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGAATGGAATAAAGCACTAGGTCAAGACATTTACCTCAATATAGCCATTGTAGTGCTCATCATCAAGAGTAATGATGATATTTTTCTCATCCCAACCAGC[G/A]
GCACTCACTTTCCTAAGCCTATTTATCTTTGTAAACTTTCTTTGCCATGTCTTCAAATGATTCTTAATTTGCTCACCCGTGAGAGTGCTGTTAAACCTTT
AAAGGTTTAACAGCACTCTCACGGGTGAGCAAATTAAGAATCATTTGAAGACATGGCAAAGAAAGTTTACAAAGATAAATAGGCTTAGGAAAGTGAGTGC[C/T]
GCTGGTTGGGATGAGAAAAATATCATCATTACTCTTGATGATGAGCACTACAATGGCTATATTGAGGTAAATGTCTTGACCTAGTGCTTTATTCCATTCA
| 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 | 21.80% | 0.10% | 2.39% | 75.73% | NA |
| All Indica | 2759 | 3.30% | 0.10% | 1.92% | 94.67% | NA |
| All Japonica | 1512 | 58.70% | 0.20% | 2.78% | 38.36% | NA |
| Aus | 269 | 7.80% | 0.00% | 2.97% | 89.22% | NA |
| Indica I | 595 | 2.40% | 0.00% | 2.35% | 95.29% | NA |
| Indica II | 465 | 3.90% | 0.00% | 0.22% | 95.91% | NA |
| Indica III | 913 | 1.90% | 0.00% | 2.74% | 95.40% | NA |
| Indica Intermediate | 786 | 5.50% | 0.30% | 1.65% | 92.62% | NA |
| Temperate Japonica | 767 | 87.40% | 0.40% | 3.78% | 8.47% | NA |
| Tropical Japonica | 504 | 11.70% | 0.00% | 0.40% | 87.90% | NA |
| Japonica Intermediate | 241 | 65.60% | 0.00% | 4.56% | 29.88% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 8.33% | 90.62% | NA |
| Intermediate | 90 | 31.10% | 0.00% | 2.22% | 66.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216387459 | G -> DEL | LOC_Os12g27800.1 | N | frameshift_variant | Average:4.533; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1216387459 | G -> A | LOC_Os12g27800.1 | synonymous_variant ; p.Ala389Ala; LOW | synonymous_codon | Average:4.533; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |