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Detailed information for vg0225213576:

Variant ID: vg0225213576 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25213576
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


GTCCATTATCACATGATTAATTAATTATTAGCTATTTTTTAAAAAAAATAAATTAATATGATTTTTTTTAAAACGTACCGTTTATCCATTTGAAAAGTGT[G/A]
CGCGTGAAAAACGTAGAAGGGAGTTGGAAGCTGGGAGATCTGAACACACCCTATGTGGGATAGTAACTAAACACTTAAACATTTAGAGCAGGTACAACAG

Reverse complement sequence

CTGTTGTACCTGCTCTAAATGTTTAAGTGTTTAGTTACTATCCCACATAGGGTGTGTTCAGATCTCCCAGCTTCCAACTCCCTTCTACGTTTTTCACGCG[C/T]
ACACTTTTCAAATGGATAAACGGTACGTTTTAAAAAAAATCATATTAATTTATTTTTTTTAAAAAATAGCTAATAATTAATTAATCATGTGATAATGGAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 61.90% 38.10% 0.06% 0.00% NA
All Indica  2759 42.80% 57.00% 0.11% 0.00% NA
All Japonica  1512 94.70% 5.30% 0.00% 0.00% NA
Aus  269 74.00% 26.00% 0.00% 0.00% NA
Indica I  595 25.40% 74.50% 0.17% 0.00% NA
Indica II  465 49.90% 50.10% 0.00% 0.00% NA
Indica III  913 46.50% 53.30% 0.11% 0.00% NA
Indica Intermediate  786 47.60% 52.30% 0.13% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 86.90% 13.10% 0.00% 0.00% NA
Japonica Intermediate  241 95.40% 4.60% 0.00% 0.00% NA
VI/Aromatic  96 57.30% 42.70% 0.00% 0.00% NA
Intermediate  90 62.20% 37.80% 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
vg0225213576 G -> A LOC_Os02g41961.1 intron_variant ; MODIFIER silent_mutation Average:63.733; most accessible tissue: Minghui63 root, score: 81.14 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225213576 NA 1.07E-06 mr1042_2 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
vg0225213576 NA 4.60E-06 mr1291_2 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
vg0225213576 3.99E-06 6.94E-11 mr1457_2 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
vg0225213576 NA 1.13E-06 mr1479_2 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
vg0225213576 NA 7.94E-06 mr1677_2 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
vg0225213576 NA 3.28E-08 mr1690_2 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
vg0225213576 NA 3.78E-06 mr1892_2 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