| Variant ID: vg1120596229 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20596229 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AAGGTCCAAACCAACCTGGAATCGACATAGATGTTTTCCTTGAGCCTTTGATGGAGGACATGGAGGAGCTTTGGAAAGAGGGGTTACAACTATGGGATGA[G/A]
TTTAAGCGGGAGCACTTCAATCTACGTGCGATCATATTCGTTACCATCAATGACCTACCTGCAAACTTTTCATTATCTGGGCAGATTAAAGGGAAGACTG
CAGTCTTCCCTTTAATCTGCCCAGATAATGAAAAGTTTGCAGGTAGGTCATTGATGGTAACGAATATGATCGCACGTAGATTGAAGTGCTCCCGCTTAAA[C/T]
TCATCCCATAGTTGTAACCCCTCTTTCCAAAGCTCCTCCATGTCCTCCATCAAAGGCTCAAGGAAAACATCTATGTCGATTCCAGGTTGGTTTGGACCTT
| 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 | 30.00% | 0.10% | 4.76% | 65.17% | NA |
| All Indica | 2759 | 13.40% | 0.00% | 4.89% | 81.73% | NA |
| All Japonica | 1512 | 59.90% | 0.30% | 4.83% | 34.92% | NA |
| Aus | 269 | 5.90% | 0.00% | 4.83% | 89.22% | NA |
| Indica I | 595 | 48.20% | 0.00% | 3.19% | 48.57% | NA |
| Indica II | 465 | 1.70% | 0.00% | 4.09% | 94.19% | NA |
| Indica III | 913 | 2.40% | 0.00% | 6.02% | 91.57% | NA |
| Indica Intermediate | 786 | 6.60% | 0.00% | 5.34% | 88.04% | NA |
| Temperate Japonica | 767 | 74.30% | 0.70% | 5.48% | 19.56% | NA |
| Tropical Japonica | 504 | 49.40% | 0.00% | 3.17% | 47.42% | NA |
| Japonica Intermediate | 241 | 36.10% | 0.00% | 6.22% | 57.68% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 1.04% | 9.38% | NA |
| Intermediate | 90 | 43.30% | 0.00% | 3.33% | 53.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120596229 | G -> A | LOC_Os11g35130.1 | synonymous_variant ; p.Glu300Glu; LOW | synonymous_codon | Average:5.97; most accessible tissue: Zhenshan97 flower, score: 13.891 | N | N | N | N |
| vg1120596229 | G -> DEL | LOC_Os11g35130.1 | N | frameshift_variant | Average:5.97; most accessible tissue: Zhenshan97 flower, score: 13.891 | N | N | N | N |