Variant ID: vg0133435968 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 33435968 |
Reference Allele: A | Alternative Allele: C |
Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 286. )
ATTATTGAGATAAGTATCGCTGGATGGCCGATATAGCCTTCTGCCTAATCTGCTCTACTTCTTCTATGGCTTGGGCATCCTGAGCGTCGGTTCCAGGGAT[A/C]
ACTTTCAGAGACTTGGTCAGATCAGCAACATGCTTGATAGCCGATTTGAGTCTTGCTTTCTGTTTTTCAATAGACTTTGGGAGATCGGCTAGTTTTTTGT
ACAAAAAACTAGCCGATCTCCCAAAGTCTATTGAAAAACAGAAAGCAAGACTCAAATCGGCTATCAAGCATGTTGCTGATCTGACCAAGTCTCTGAAAGT[T/G]
ATCCCTGGAACCGACGCTCAGGATGCCCAAGCCATAGAAGAAGTAGAGCAGATTAGGCAGAAGGCTATATCGGCCATCCAGCGATACTTATCTCAATAAT
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 | 98.80% | 0.10% | 0.28% | 0.80% | NA |
All Indica | 2759 | 98.00% | 0.10% | 0.47% | 1.38% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Indica I | 595 | 98.70% | 0.00% | 0.67% | 0.67% | NA |
Indica II | 465 | 99.80% | 0.00% | 0.00% | 0.22% | NA |
Indica III | 913 | 96.20% | 0.40% | 0.77% | 2.63% | NA |
Indica Intermediate | 786 | 98.60% | 0.00% | 0.25% | 1.15% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0133435968 | A -> C | LOC_Os01g57810.1 | synonymous_variant ; p.Val746Val; LOW | N | Average:23.017; most accessible tissue: Callus, score: 35.965 | N | N | N | N |
vg0133435968 | A -> C | LOC_Os01g57800.1 | downstream_gene_variant ; 552.0bp to feature; MODIFIER | N | Average:23.017; most accessible tissue: Callus, score: 35.965 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0133435968 | 6.93E-06 | NA | mr1531 | 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 |