| Variant ID: vg0114539569 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14539569 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, C: 0.02, others allele: 0.00, population size: 105. )
AGAAACTGTTGAAGATTTTGATGAAGTGGAGAAGCTTGGACAAGGGTTTACATCGGCCGATCCATTGGAAGAAGTAGACATAGGTGATGGAACTAAACCA[A/C]
GGCTGACTTTTGTAGACAAAAACATGAGAGCCGATTATAAGGTTAAGATAATCGAGCTACTTAAAGAGTATGTTGATTGCTTTGCATGGAAGTACCATGA
TCATGGTACTTCCATGCAAAGCAATCAACATACTCTTTAAGTAGCTCGATTATCTTAACCTTATAATCGGCTCTCATGTTTTTGTCTACAAAAGTCAGCC[T/G]
TGGTTTAGTTCCATCACCTATGTCTACTTCTTCCAATGGATCGGCCGATGTAAACCCTTGTCCAAGCTTCTCCACTTCATCAAAATCTTCAACAGTTTCT
| 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 | 76.40% | 4.80% | 7.00% | 11.79% | NA |
| All Indica | 2759 | 84.60% | 7.90% | 5.65% | 1.85% | NA |
| All Japonica | 1512 | 62.20% | 0.10% | 9.06% | 28.64% | NA |
| Aus | 269 | 69.50% | 1.10% | 8.55% | 20.82% | NA |
| Indica I | 595 | 76.00% | 5.50% | 14.79% | 3.70% | NA |
| Indica II | 465 | 90.80% | 3.00% | 5.59% | 0.65% | NA |
| Indica III | 913 | 90.40% | 9.10% | 0.44% | 0.11% | NA |
| Indica Intermediate | 786 | 80.80% | 11.20% | 4.83% | 3.18% | NA |
| Temperate Japonica | 767 | 86.30% | 0.10% | 1.43% | 12.13% | NA |
| Tropical Japonica | 504 | 28.20% | 0.00% | 19.44% | 52.38% | NA |
| Japonica Intermediate | 241 | 56.80% | 0.00% | 11.62% | 31.54% | NA |
| VI/Aromatic | 96 | 78.10% | 0.00% | 11.46% | 10.42% | NA |
| Intermediate | 90 | 83.30% | 4.40% | 4.44% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114539569 | A -> DEL | LOC_Os01g25650.1 | N | frameshift_variant | Average:13.318; most accessible tissue: Callus, score: 32.375 | N | N | N | N |
| vg0114539569 | A -> C | LOC_Os01g25650.1 | synonymous_variant ; p.Arg956Arg; LOW | synonymous_codon | Average:13.318; most accessible tissue: Callus, score: 32.375 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0114539569 | 8.09E-07 | 5.47E-07 | mr1371 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0114539569 | 1.26E-06 | 1.26E-06 | mr1412 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0114539569 | 4.41E-06 | 4.41E-06 | mr1492 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0114539569 | 7.35E-06 | 7.35E-06 | mr1605 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |