| Variant ID: vg1115080358 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 15080358 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GGAATGGATTCGATGAAAGTTACATACAGTGGGTTTACCACGGTGAAGATTCAGATGATGACAATGTCACGGGAAGATTCAGAAGAACGTAAGGAAAGGG[A/G]
AATGCTACGGGAGGATATTCTCAAAATGATTACTACGCAAAGCGTAGCATCGGAACAACAGGTAATGATTGCCAAAATGTTCACATTCACCAATATTTGA
TCAAATATTGGTGAATGTGAACATTTTGGCAATCATTACCTGTTGTTCCGATGCTACGCTTTGCGTAGTAATCATTTTGAGAATATCCTCCCGTAGCATT[T/C]
CCCTTTCCTTACGTTCTTCTGAATCTTCCCGTGACATTGTCATCATCTGAATCTTCACCGTGGTAAACCCACTGTATGTAACTTTCATCGAATCCATTCC
| 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 | 57.50% | 5.70% | 16.34% | 20.48% | NA |
| All Indica | 2759 | 39.80% | 0.60% | 26.02% | 33.60% | NA |
| All Japonica | 1512 | 79.80% | 16.40% | 2.65% | 1.19% | NA |
| Aus | 269 | 94.80% | 0.00% | 0.74% | 4.46% | NA |
| Indica I | 595 | 27.60% | 1.20% | 18.99% | 52.27% | NA |
| Indica II | 465 | 40.90% | 0.00% | 32.90% | 26.24% | NA |
| Indica III | 913 | 43.90% | 0.00% | 28.70% | 27.38% | NA |
| Indica Intermediate | 786 | 43.60% | 1.10% | 24.17% | 31.04% | NA |
| Temperate Japonica | 767 | 67.00% | 28.20% | 3.52% | 1.30% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.60% | 0.60% | NA |
| Japonica Intermediate | 241 | 80.50% | 13.30% | 4.15% | 2.07% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 72.20% | 2.20% | 13.33% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1115080358 | A -> DEL | LOC_Os11g26350.1 | N | frameshift_variant | Average:10.971; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1115080358 | A -> G | LOC_Os11g26350.1 | missense_variant ; p.Glu92Gly; MODERATE | nonsynonymous_codon ; E92G | Average:10.971; most accessible tissue: Zhenshan97 panicle, score: 16.188 | unknown | unknown | DELETERIOUS | 0.00 |