| Variant ID: vg1216389416 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16389416 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GATACAAGTTGTATCGTTCCACCAAATTTTCGTTTCTAGGTACTCAATTCTTTTTCTATCCCTTTCAACCATTGGGCCATATCTAATACCTTCTCTCCTT[G/A]
AACACCTCTTTCTTTTTCTAGACCTAATAATCATGGCCATCATCGACAACAATAAATTTGTAGCTGCAATACAAACTAAAAGCTTGGTCCTCTTGTCCAT
ATGGACAAGAGGACCAAGCTTTTAGTTTGTATTGCAGCTACAAATTTATTGTTGTCGATGATGGCCATGATTATTAGGTCTAGAAAAAGAAAGAGGTGTT[C/T]
AAGGAGAGAAGGTATTAGATATGGCCCAATGGTTGAAAGGGATAGAAAAAGAATTGAGTACCTAGAAACGAAAATTTGGTGGAACGATACAACTTGTATC
| 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 | 19.60% | 0.70% | 4.72% | 74.99% | NA |
| All Indica | 2759 | 2.40% | 1.20% | 2.68% | 93.77% | NA |
| All Japonica | 1512 | 50.90% | 0.10% | 5.82% | 43.19% | NA |
| Aus | 269 | 21.20% | 0.00% | 15.24% | 63.57% | NA |
| Indica I | 595 | 0.80% | 0.00% | 0.67% | 98.49% | NA |
| Indica II | 465 | 3.70% | 4.70% | 8.39% | 83.23% | NA |
| Indica III | 913 | 0.80% | 0.20% | 0.55% | 98.47% | NA |
| Indica Intermediate | 786 | 4.70% | 1.00% | 3.31% | 90.97% | NA |
| Temperate Japonica | 767 | 73.40% | 0.00% | 10.56% | 16.04% | NA |
| Tropical Japonica | 504 | 10.70% | 0.00% | 0.40% | 88.89% | NA |
| Japonica Intermediate | 241 | 63.50% | 0.40% | 2.07% | 34.02% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 16.67% | 73.96% | NA |
| Intermediate | 90 | 26.70% | 0.00% | 4.44% | 68.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216389416 | G -> DEL | LOC_Os12g27800.1 | N | frameshift_variant | Average:5.078; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |
| vg1216389416 | G -> A | LOC_Os12g27800.1 | missense_variant ; p.Ser14Leu; MODERATE | nonsynonymous_codon ; S14L | Average:5.078; most accessible tissue: Zhenshan97 flower, score: 9.663 | unknown | unknown | TOLERATED | 0.08 |