Variant ID: vg0127445565 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 27445565 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.00, others allele: 0.00, population size: 241. )
GGGTACGGCGTTTGCTCCAGTGACCACAATACGATTGGGATGTCTGCTTCGTGTAAATTGGCGGTAATGTGGAGGTCGACTTTGCCTTGGTTGCAGGCAG[T/C]
CCCTCGAGTAATGCCCTGGTTCTTTGCAGTTGTAACAAATCAACGTCTTCTTTACTGAGCTGTCCATCTGGGGACGATCATTTTGACTTGGAGTTGGAAT
ATTCCAACTCCAAGTCAAAATGATCGTCCCCAGATGGACAGCTCAGTAAAGAAGACGTTGATTTGTTACAACTGCAAAGAACCAGGGCATTACTCGAGGG[A/G]
CTGCCTGCAACCAAGGCAAAGTCGACCTCCACATTACCGCCAATTTACACGAAGCAGACATCCCAATCGTATTGTGGTCACTGGAGCAAACGCCGTACCC
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 | 65.80% | 6.80% | 2.03% | 25.39% | NA |
All Indica | 2759 | 46.20% | 9.80% | 2.43% | 41.57% | NA |
All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.07% | NA |
Aus | 269 | 55.80% | 17.80% | 10.41% | 15.99% | NA |
Indica I | 595 | 30.80% | 4.40% | 3.87% | 61.01% | NA |
Indica II | 465 | 41.10% | 9.20% | 1.72% | 47.96% | NA |
Indica III | 913 | 56.20% | 10.00% | 1.86% | 31.98% | NA |
Indica Intermediate | 786 | 49.20% | 14.10% | 2.42% | 34.22% | NA |
Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | 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 | 86.70% | 2.20% | 1.11% | 10.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0127445565 | T -> DEL | LOC_Os01g47960.1 | N | frameshift_variant | Average:6.962; most accessible tissue: Callus, score: 28.943 | N | N | N | N |
vg0127445565 | T -> C | LOC_Os01g47960.1 | missense_variant ; p.Asp459Gly; MODERATE | nonsynonymous_codon ; D459G | Average:6.962; most accessible tissue: Callus, score: 28.943 | possibly damaging | 1.551 | DELETERIOUS | 0.05 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0127445565 | 5.75E-09 | 4.04E-15 | mr1216 | 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 |
vg0127445565 | 2.98E-08 | 3.76E-15 | mr1216 | 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 |