| Variant ID: vg1105161115 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5161115 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCGTGGGTTTGGCTCCCCGTCGTCACCGCTAACACTCGGAGAGAGGTTGTGCGCCTTTGCTTGTTC[A/G]
GCCATTGGGCTGAACAGGAAAAGCTTGGCGCACACGAAAGAGTGCGAGAGCTTAGAAGAACACACGCAGAACCCCCTACCTGGCGCGCCAGATGACGGCG
CGCCGTCATCTGGCGCGCCAGGTAGGGGGTTCTGCGTGTGTTCTTCTAAGCTCTCGCACTCTTTCGTGTGCGCCAAGCTTTTCCTGTTCAGCCCAATGGC[T/C]
GAACAAGCAAAGGCGCACAACCTCTCTCCGAGTGTTAGCGGTGACGACGGGGAGCCAAACCCACGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCC
| 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 | 33.60% | 30.20% | 19.85% | 16.38% | NA |
| All Indica | 2759 | 10.10% | 41.40% | 27.22% | 21.24% | NA |
| All Japonica | 1512 | 83.70% | 0.80% | 6.15% | 9.33% | NA |
| Aus | 269 | 0.70% | 81.80% | 11.90% | 5.58% | NA |
| Indica I | 595 | 6.20% | 38.50% | 34.79% | 20.50% | NA |
| Indica II | 465 | 5.20% | 42.20% | 21.94% | 30.75% | NA |
| Indica III | 913 | 8.90% | 47.50% | 25.85% | 17.74% | NA |
| Indica Intermediate | 786 | 17.40% | 36.10% | 26.21% | 20.23% | NA |
| Temperate Japonica | 767 | 88.70% | 0.30% | 2.48% | 8.60% | NA |
| Tropical Japonica | 504 | 79.40% | 1.20% | 9.92% | 9.52% | NA |
| Japonica Intermediate | 241 | 77.20% | 1.70% | 9.96% | 11.20% | NA |
| VI/Aromatic | 96 | 10.40% | 31.20% | 40.62% | 17.71% | NA |
| Intermediate | 90 | 34.40% | 23.30% | 25.56% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105161115 | A -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:6.249; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg1105161115 | A -> G | LOC_Os11g09660.1 | synonymous_variant ; p.Ala2Ala; LOW | synonymous_codon | Average:6.249; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |