Variant ID: vg0107026972 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 7026972 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 291. )
ATTCTTCTTATTCTTATGTATAGATAAATAACGCTGGCACAAACAAAGGTTTTAGGCCACTGGTAAACTTTTCAGATGAAGATATTTCTCAGGTACGTTA[A/G]
TTATCTTCGGAAAATCAGAGTCTTTTCCATTCTAATAGAGTTCATAGAACTATATTCGTCATGCAACCTGACTTAGTTATTTCATCTTATTTTTCTTTCT
AGAAAGAAAAATAAGATGAAATAACTAAGTCAGGTTGCATGACGAATATAGTTCTATGAACTCTATTAGAATGGAAAAGACTCTGATTTTCCGAAGATAA[T/C]
TAACGTACCTGAGAAATATCTTCATCTGAAAAGTTTACCAGTGGCCTAAAACCTTTGTTTGTGCCAGCGTTATTTATCTATACATAAGAATAAGAAGAAT
Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 83.50% | 16.50% | 0.06% | 0.00% | NA |
All Indica | 2759 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 52.20% | 47.70% | 0.13% | 0.00% | NA |
Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 36.90% | 63.10% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 78.80% | 21.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 45.20% | 53.90% | 0.83% | 0.00% | NA |
VI/Aromatic | 96 | 69.80% | 30.20% | 0.00% | 0.00% | NA |
Intermediate | 90 | 78.90% | 20.00% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0107026972 | A -> G | LOC_Os01g12710.1 | intron_variant ; MODIFIER | silent_mutation | Average:56.978; most accessible tissue: Callus, score: 77.578 | N | N | N | N |
vg0107026972 | A -> G | LOC_Os01g12710.2 | intron_variant ; MODIFIER | silent_mutation | Average:56.978; most accessible tissue: Callus, score: 77.578 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0107026972 | 7.61E-08 | NA | mr1679 | 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 |