| Variant ID: vg0114526976 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14526976 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.01, others allele: 0.00, population size: 286. )
CACAATCATGTGCCTTGTGTTCTGGCGAAAAAGGTTACTATCATGTGCGGATTGCATATTTCCAAGTCTTTGGCTTCATTAATTTTGGCCCTGGTCACAG[A/G]
TGATGATGTTGGAAGACATACGTATAAGTTAATGTACCATGAAAAATATAAATCTATATATAGGCATTACACAAAAAGTATCATAGTATATATCTTGAGT
ACTCAAGATATATACTATGATACTTTTTGTGTAATGCCTATATATAGATTTATATTTTTCATGGTACATTAACTTATACGTATGTCTTCCAACATCATCA[T/C]
CTGTGACCAGGGCCAAAATTAATGAAGCCAAAGACTTGGAAATATGCAATCCGCACATGATAGTAACCTTTTTCGCCAGAACACAAGGCACATGATTGTG
| 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 | 83.30% | 12.40% | 0.30% | 3.94% | NA |
| All Indica | 2759 | 74.20% | 18.70% | 0.51% | 6.60% | NA |
| All Japonica | 1512 | 97.50% | 2.40% | 0.00% | 0.07% | NA |
| Aus | 269 | 88.10% | 11.20% | 0.00% | 0.74% | NA |
| Indica I | 595 | 85.40% | 9.60% | 0.17% | 4.87% | NA |
| Indica II | 465 | 83.90% | 13.10% | 0.43% | 2.58% | NA |
| Indica III | 913 | 62.70% | 29.00% | 0.22% | 8.11% | NA |
| Indica Intermediate | 786 | 73.50% | 16.80% | 1.15% | 8.52% | NA |
| Temperate Japonica | 767 | 98.70% | 1.20% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 5.60% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114526976 | A -> G | LOC_Os01g25630.1 | intron_variant ; MODIFIER | silent_mutation | Average:46.758; most accessible tissue: Callus, score: 80.0 | N | N | N | N |
| vg0114526976 | A -> DEL | N | N | silent_mutation | Average:46.758; most accessible tissue: Callus, score: 80.0 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0114526976 | NA | 1.94E-09 | Grain_thickness | Ind_All | Not | 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 |
| vg0114526976 | NA | 2.10E-09 | Grain_weight | Ind_All | Not | 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 |