| Variant ID: vg0514763041 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 14763041 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 254. )
GTTCAACATCACAGATTCAGATATTCTCATTTTCTGTGTTCTTTAACCAGTGGCACAATGTGTGCTATCAGTGTAATTAAAATAGGGATTTCTTAATATG[T/C]
ATTGCTCTTTGGATGATTTCAGTATTTCAACGAGTTCTTAATAGACCTTTTTTTTTCATCTGTGCATGCAAGAGGATGCAACCTACTTGGGATGGTGGCA
TGCCACCATCCCAAGTAGGTTGCATCCTCTTGCATGCACAGATGAAAAAAAAAGGTCTATTAAGAACTCGTTGAAATACTGAAATCATCCAAAGAGCAAT[A/G]
CATATTAAGAAATCCCTATTTTAATTACACTGATAGCACACATTGTGCCACTGGTTAAAGAACACAGAAAATGAGAATATCTGAATCTGTGATGTTGAAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.20% | 38.70% | 2.35% | 4.74% | NA |
| All Indica | 2759 | 27.80% | 63.90% | 3.70% | 4.57% | NA |
| All Japonica | 1512 | 92.90% | 2.20% | 0.20% | 4.76% | NA |
| Aus | 269 | 88.10% | 4.10% | 1.49% | 6.32% | NA |
| Indica I | 595 | 15.30% | 79.30% | 4.03% | 1.34% | NA |
| Indica II | 465 | 23.70% | 66.90% | 3.23% | 6.24% | NA |
| Indica III | 913 | 37.00% | 54.70% | 2.41% | 5.91% | NA |
| Indica Intermediate | 786 | 29.00% | 61.30% | 5.22% | 4.45% | NA |
| Temperate Japonica | 767 | 97.50% | 0.90% | 0.00% | 1.56% | NA |
| Tropical Japonica | 504 | 83.70% | 4.40% | 0.40% | 11.51% | NA |
| Japonica Intermediate | 241 | 97.10% | 1.70% | 0.41% | 0.83% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 65.60% | 22.20% | 2.22% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0514763041 | T -> DEL | N | N | silent_mutation | Average:19.926; most accessible tissue: Callus, score: 57.754 | N | N | N | N |
| vg0514763041 | T -> C | LOC_Os05g25390-LOC_Os05g25400 | intergenic_region ; MODIFIER | silent_mutation | Average:19.926; most accessible tissue: Callus, score: 57.754 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0514763041 | 6.03E-06 | 6.03E-06 | mr1690_2 | 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 |
| vg0514763041 | 2.44E-06 | 2.44E-06 | mr1991_2 | 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 |