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Detailed information for vg0624615989:

Variant ID: vg0624615989 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 24615989
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


ATAAATTTACAAGTAAAGCAAGTGTGAGAAATAAAATGACATGGTTAAATTTAATTTTTTTAAATTCTCCATGATTAGTTACACTCGTTAAAATTTTATT[G/A]
GAATTTTCAGAGCTTAATTGCTAATTTTAATAATACAAACATCATTTAAAAATTATTTAATTAAAAAAGAAAGAAACTACTTCCTTTTAGGTTTGCTTCG

Reverse complement sequence

CGAAGCAAACCTAAAAGGAAGTAGTTTCTTTCTTTTTTAATTAAATAATTTTTAAATGATGTTTGTATTATTAAAATTAGCAATTAAGCTCTGAAAATTC[C/T]
AATAAAATTTTAACGAGTGTAACTAATCATGGAGAATTTAAAAAAATTAAATTTAACCATGTCATTTTATTTCTCACACTTGCTTTACTTGTAAATTTAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.20% 32.50% 0.34% 0.00% NA
All Indica  2759 97.00% 2.50% 0.47% 0.00% NA
All Japonica  1512 11.60% 88.40% 0.00% 0.00% NA
Aus  269 95.90% 4.10% 0.00% 0.00% NA
Indica I  595 98.00% 0.70% 1.34% 0.00% NA
Indica II  465 96.60% 3.20% 0.22% 0.00% NA
Indica III  913 98.20% 1.60% 0.11% 0.00% NA
Indica Intermediate  786 95.00% 4.60% 0.38% 0.00% NA
Temperate Japonica  767 2.50% 97.50% 0.00% 0.00% NA
Tropical Japonica  504 29.00% 71.00% 0.00% 0.00% NA
Japonica Intermediate  241 4.10% 95.90% 0.00% 0.00% NA
VI/Aromatic  96 16.70% 83.30% 0.00% 0.00% NA
Intermediate  90 55.60% 41.10% 3.33% 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
vg0624615989 G -> A LOC_Os06g41140-LOC_Os06g41150 intergenic_region ; MODIFIER silent_mutation Average:23.069; most accessible tissue: Zhenshan97 panicle, score: 39.652 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0624615989 NA 1.72E-18 mr1077 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
vg0624615989 NA 5.60E-29 mr1256 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
vg0624615989 NA 4.70E-08 mr1583 Jap_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
vg0624615989 NA 1.01E-37 mr1601 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
vg0624615989 NA 2.10E-08 mr1623_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
vg0624615989 NA 2.85E-36 mr1689_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
vg0624615989 1.13E-10 NA mr1850_2 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
vg0624615989 4.84E-07 3.78E-09 mr1850_2 Jap_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