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Detailed information for vg0622281780:

Variant ID: vg0622281780 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 22281780
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.02, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


TTGTTTAATTTGTCGTTGGCACATATTATGTTATGTACGATCGCCAAGACTTTTGCGCCTTAGCGCATGTGAAACGTTTTTAATTGGGCCATTTATCGAT[C/A]
GATCAATCGATGTCTTTAATCTCTGGATTCTCACCTAAAAGAGAAGAATTCATGCATCTCGCAAGCTAGAATTCTTCAAGATTTCAAATCTTCAGCTAAC

Reverse complement sequence

GTTAGCTGAAGATTTGAAATCTTGAAGAATTCTAGCTTGCGAGATGCATGAATTCTTCTCTTTTAGGTGAGAATCCAGAGATTAAAGACATCGATTGATC[G/T]
ATCGATAAATGGCCCAATTAAAAACGTTTCACATGCGCTAAGGCGCAAAAGTCTTGGCGATCGTACATAACATAATATGTGCCAACGACAAATTAAACAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.50% 11.40% 0.15% 0.00% NA
All Indica  2759 86.90% 12.90% 0.22% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 44.20% 55.40% 0.37% 0.00% NA
Indica I  595 86.10% 13.40% 0.50% 0.00% NA
Indica II  465 95.10% 4.90% 0.00% 0.00% NA
Indica III  913 85.50% 14.30% 0.11% 0.00% NA
Indica Intermediate  786 84.40% 15.40% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 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 68.80% 31.20% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0622281780 C -> A LOC_Os06g37630.1 intron_variant ; MODIFIER silent_mutation Average:60.336; most accessible tissue: Callus, score: 84.894 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0622281780 NA 3.55E-09 mr1037 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0622281780 NA 2.03E-06 mr1064 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0622281780 NA 1.61E-07 mr1669 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0622281780 NA 3.41E-08 mr1887 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
vg0622281780 8.41E-06 1.42E-08 mr1887 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