| Variant ID: vg1126836664 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26836664 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CAAAATAACAAAGAAATAGGAGCCAGAGAAAGAGAAGGTATGACATAGACGAGAGAAATAGATATATTTGATGGCTGGTCCATTTGTTCAATTACCTCGG[A/C]
TAACTCTTTGTACTCTACTTCTGCTATAAGCGATAGAAATTTCCACATTAAACCAAAAAAATAATTGTTCAAGTAAAAATACAATTTAAAAGTAACTAAA
TTTAGTTACTTTTAAATTGTATTTTTACTTGAACAATTATTTTTTTGGTTTAATGTGGAAATTTCTATCGCTTATAGCAGAAGTAGAGTACAAAGAGTTA[T/G]
CCGAGGTAATTGAACAAATGGACCAGCCATCAAATATATCTATTTCTCTCGTCTATGTCATACCTTCTCTTTCTCTGGCTCCTATTTCTTTGTTATTTTG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 76.10% | 8.50% | 4.25% | 11.17% | NA |
| All Indica | 2759 | 67.90% | 10.40% | 5.55% | 16.20% | NA |
| All Japonica | 1512 | 90.60% | 4.60% | 1.39% | 3.44% | NA |
| Aus | 269 | 70.30% | 13.00% | 8.55% | 8.18% | NA |
| Indica I | 595 | 93.30% | 1.80% | 2.86% | 2.02% | NA |
| Indica II | 465 | 57.60% | 1.90% | 1.72% | 38.71% | NA |
| Indica III | 913 | 60.60% | 19.90% | 10.62% | 8.87% | NA |
| Indica Intermediate | 786 | 63.20% | 10.70% | 3.94% | 22.14% | NA |
| Temperate Japonica | 767 | 95.70% | 0.50% | 0.26% | 3.52% | NA |
| Tropical Japonica | 504 | 82.90% | 12.90% | 1.39% | 2.78% | NA |
| Japonica Intermediate | 241 | 90.50% | 0.00% | 4.98% | 4.56% | NA |
| VI/Aromatic | 96 | 89.60% | 9.40% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 3.30% | 3.33% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126836664 | A -> DEL | N | N | silent_mutation | Average:44.248; most accessible tissue: Minghui63 root, score: 67.73 | N | N | N | N |
| vg1126836664 | A -> C | LOC_Os11g44380.1 | upstream_gene_variant ; 3810.0bp to feature; MODIFIER | silent_mutation | Average:44.248; most accessible tissue: Minghui63 root, score: 67.73 | N | N | N | N |
| vg1126836664 | A -> C | LOC_Os11g44380-LOC_Os11g44390 | intergenic_region ; MODIFIER | silent_mutation | Average:44.248; most accessible tissue: Minghui63 root, score: 67.73 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1126836664 | NA | 8.78E-08 | Grain_thickness | Ind_All | YES | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |