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Detailed information for vg0715150413:

Variant ID: vg0715150413 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 15150413
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:


ATCATCCACTGTGTCCTTGTTGTAGACATCTGAACCCTCCACGACGCCCTCAAAATAATAGCTTGGGTTCTCCATCTTCAATTGGCTGTATATCAGAGTC[G/A]
GACACTTTTAGAAAATCTCCATCCCAAACTTTTCCAGATAAACAATCAAGACCATCCATCTCCCAAAGAGCTAAATCGGCACTGGCAACATTGACTGACC

Reverse complement sequence

GGTCAGTCAATGTTGCCAGTGCCGATTTAGCTCTTTGGGAGATGGATGGTCTTGATTGTTTATCTGGAAAAGTTTGGGATGGAGATTTTCTAAAAGTGTC[C/T]
GACTCTGATATACAGCCAATTGAAGATGGAGAACCCAAGCTATTATTTTGAGGGCGTCGTGGAGGGTTCAGATGTCTACAACAAGGACACAGTGGATGAT

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 99.30% 0.30% 0.04% 0.32% NA
All Indica  2759 99.50% 0.50% 0.04% 0.00% NA
All Japonica  1512 98.90% 0.10% 0.07% 0.99% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.50% 0.40% 0.11% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 97.80% 0.10% 0.13% 1.96% 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 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0715150413 G -> A LOC_Os07g26350.1 downstream_gene_variant ; 2991.0bp to feature; MODIFIER N Average:16.621; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 N N N N
vg0715150413 G -> A LOC_Os07g26360.1 intron_variant ; MODIFIER N Average:16.621; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0715150413 6.52E-06 3.77E-06 mr1971_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