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Detailed information for vg0716252921:

Variant ID: vg0716252921 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 16252921
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


GTTGAGCGAAATGATTTTTTTTCGCGAACCTTTTTTTAGGCTGCGTTTTTTCTTGCCATTTTTTTTCCTCGAATCGGATTGCTCTTTTTTCTCGTTGCGT[G/A]
GAACCGGATTTTTGTTTCTCGCGTTACGTTGTGCCAAACTTTTTCTCATGGAATCATAGGAAAATGCTTACGGTCGAACGTCCGATCCAGCTAAAAAGAT

Reverse complement sequence

ATCTTTTTAGCTGGATCGGACGTTCGACCGTAAGCATTTTCCTATGATTCCATGAGAAAAAGTTTGGCACAACGTAACGCGAGAAACAAAAATCCGGTTC[C/T]
ACGCAACGAGAAAAAAGAGCAATCCGATTCGAGGAAAAAAAATGGCAAGAAAAAACGCAGCCTAAAAAAAGGTTCGCGAAAAAAAATCATTTCGCTCAAC

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 74.20% 25.80% 0.06% 0.02% NA
All Indica  2759 56.70% 43.20% 0.11% 0.04% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 53.80% 46.10% 0.00% 0.17% NA
Indica II  465 85.20% 14.80% 0.00% 0.00% NA
Indica III  913 35.70% 64.30% 0.00% 0.00% NA
Indica Intermediate  786 66.30% 33.30% 0.38% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 76.70% 23.30% 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
vg0716252921 G -> DEL N N silent_mutation Average:41.58; most accessible tissue: Minghui63 flag leaf, score: 64.867 N N N N
vg0716252921 G -> A LOC_Os07g27834-LOC_Os07g27850 intergenic_region ; MODIFIER silent_mutation Average:41.58; most accessible tissue: Minghui63 flag leaf, score: 64.867 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0716252921 NA 2.09E-09 mr1705 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
vg0716252921 6.30E-06 6.21E-08 mr1705 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
vg0716252921 NA 2.02E-06 mr1715 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
vg0716252921 NA 6.11E-11 mr1705_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
vg0716252921 NA 4.96E-09 mr1705_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