Variant ID: vg0806619995 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 6619995 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 254. )
GATGTTGCAGGACGTCAAGGAGGACTGTGAAATTGAAAAGGAGGTCCAGAAATTGGAGCGTATGTTAGCGGACCACAGGACACCGTTATACCCAGGTTGC[G/A]
AGTAGGGGCATAAAAAGTTGGGTAACACTATGGAATTCTTGCAATGGAAGGCAAAATGTGGTCTGAGTGACAAGGCATTTGGCGACTTATTGAAACTAGT
ACTAGTTTCAATAAGTCGCCAAATGCCTTGTCACTCAGACCACATTTTGCCTTCCATTGCAAGAATTCCATAGTGTTACCCAACTTTTTATGCCCCTACT[C/T]
GCAACCTGGGTATAACGGTGTCCTGTGGTCCGCTAACATACGCTCCAATTTCTGGACCTCCTTTTCAATTTCACAGTCCTCCTTGACGTCCTGCAACATC
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 | 90.40% | 0.10% | 3.96% | 5.54% | NA |
All Indica | 2759 | 83.80% | 0.10% | 6.74% | 9.35% | NA |
All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.07% | NA |
Aus | 269 | 99.30% | 0.40% | 0.37% | 0.00% | NA |
Indica I | 595 | 69.10% | 0.20% | 5.21% | 25.55% | NA |
Indica II | 465 | 90.80% | 0.20% | 3.44% | 5.59% | NA |
Indica III | 913 | 86.70% | 0.00% | 11.28% | 1.97% | NA |
Indica Intermediate | 786 | 87.40% | 0.10% | 4.58% | 7.89% | 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 | 96.70% | 0.00% | 0.00% | 3.33% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0806619995 | G -> A | LOC_Os08g11260.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.052; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
vg0806619995 | G -> DEL | N | N | silent_mutation | Average:14.052; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0806619995 | 2.76E-06 | 2.63E-06 | mr1856 | 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 |