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Detailed information for vg0516076751:

Variant ID: vg0516076751 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 16076751
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: 336. )

Flanking Sequence (100 bp) in Reference Genome:


CAAATTCGTCGGGTAAGACACACTTAAGGAGTTCGAGTTCCTTAGCCATGGTTTGTATCTCATGAGCCTATTCGACTACAAAATGGTTGTCAGCCATCTT[G/A]
TAGTCATGAAACTGCTCCATGATATACAGATCATTGCTAGCATCAGTAGCACCGAATTTAGTATTCAGTGCATCCCACAACTCCTTAGCGTCGGTCATAT

Reverse complement sequence

ATATGACCGACGCTAAGGAGTTGTGGGATGCACTGAATACTAAATTCGGTGCTACTGATGCTAGCAATGATCTGTATATCATGGAGCAGTTTCATGACTA[C/T]
AAGATGGCTGACAACCATTTTGTAGTCGAATAGGCTCATGAGATACAAACCATGGCTAAGGAACTCGAACTCCTTAAGTGTGTCTTACCCGACGAATTTG

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 96.10% 3.90% 0.02% 0.00% NA
All Indica  2759 93.30% 6.60% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 85.70% 14.10% 0.17% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 97.20% 2.80% 0.00% 0.00% NA
Indica Intermediate  786 91.50% 8.50% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0516076751 G -> A LOC_Os05g27640.1 downstream_gene_variant ; 3502.0bp to feature; MODIFIER silent_mutation Average:36.368; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 N N N N
vg0516076751 G -> A LOC_Os05g27630.1 intron_variant ; MODIFIER silent_mutation Average:36.368; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0516076751 NA 7.40E-06 mr1582_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