| Variant ID: vg1114173832 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 14173832 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GAACAGAGGAGGTCATCGAATTTTGCGTAGAATTTATCGAAGACCTTCGCCCAATCGGGGTACCTGAATCACGCCATGAAGGGAGACTACGGGGAAAGGG[A/G]
ACTCTCGGAAGGAAAGCAATAACGACGGTAGACAACAATTTATTCCGTAAAGCCCATTTCACTGTTCTGCAACACTCTTCATTGGTAGCTCCTTACATCG
CGATGTAAGGAGCTACCAATGAAGAGTGTTGCAGAACAGTGAAATGGGCTTTACGGAATAAATTGTTGTCTACCGTCGTTATTGCTTTCCTTCCGAGAGT[T/C]
CCCTTTCCCCGTAGTCTCCCTTCATGGCGTGATTCAGGTACCCCGATTGGGCGAAGGTCTTCGATAAATTCTACGCAAAATTCGATGACCTCCTCTGTTC
| 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 | 35.30% | 1.30% | 2.98% | 60.39% | NA |
| All Indica | 2759 | 3.30% | 1.40% | 4.17% | 91.19% | NA |
| All Japonica | 1512 | 96.60% | 0.10% | 0.26% | 3.04% | NA |
| Aus | 269 | 0.40% | 8.60% | 4.83% | 86.25% | NA |
| Indica I | 595 | 3.50% | 0.20% | 2.02% | 94.29% | NA |
| Indica II | 465 | 1.90% | 2.20% | 4.73% | 91.18% | NA |
| Indica III | 913 | 2.00% | 1.30% | 5.37% | 91.35% | NA |
| Indica Intermediate | 786 | 5.30% | 1.90% | 4.07% | 88.68% | NA |
| Temperate Japonica | 767 | 96.30% | 0.00% | 0.13% | 3.52% | NA |
| Tropical Japonica | 504 | 96.40% | 0.20% | 0.60% | 2.78% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 4.17% | 9.38% | NA |
| Intermediate | 90 | 36.70% | 1.10% | 5.56% | 56.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1114173832 | A -> DEL | LOC_Os11g24860.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1114173832 | A -> G | LOC_Os11g24860.1 | synonymous_variant ; p.Gly821Gly; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |