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Detailed information for vg0607014877:

Variant ID: vg0607014877 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 7014877
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: 236. )

Flanking Sequence (100 bp) in Reference Genome:


GGGTTTCACTGATATGTGGGGCCCTCGTTGACTCAGCTGCCACATTGAACAAAAATGATTCGGTTTTATAAGTTAAGAGATGACATATATCTGATTTTGC[G/A]
GTTGGGAGATGATTTTGTAATATGATGACAAGATGAGGTGACCTTCGATATACTTTTTCCCACTGCAAAATATCCAGAGATGGGTTAAGAAAGCCCTCTT

Reverse complement sequence

AAGAGGGCTTTCTTAACCCATCTCTGGATATTTTGCAGTGGGAAAAAGTATATCGAAGGTCACCTCATCTTGTCATCATATTACAAAATCATCTCCCAAC[C/T]
GCAAAATCAGATATATGTCATCTCTTAACTTATAAAACCGAATCATTTTTGTTCAATGTGGCAGCTGAGTCAACGAGGGCCCCACATATCAGTGAAACCC

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 78.20% 21.70% 0.08% 0.00% NA
All Indica  2759 63.80% 36.00% 0.14% 0.00% NA
All Japonica  1512 99.40% 0.60% 0.00% 0.00% NA
Aus  269 95.20% 4.80% 0.00% 0.00% NA
Indica I  595 68.20% 31.80% 0.00% 0.00% NA
Indica II  465 65.40% 34.00% 0.65% 0.00% NA
Indica III  913 62.30% 37.60% 0.11% 0.00% NA
Indica Intermediate  786 61.30% 38.70% 0.00% 0.00% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0607014877 G -> A LOC_Os06g12830.1 downstream_gene_variant ; 4942.0bp to feature; MODIFIER silent_mutation Average:61.541; most accessible tissue: Zhenshan97 flower, score: 79.365 N N N N
vg0607014877 G -> A LOC_Os06g12820-LOC_Os06g12830 intergenic_region ; MODIFIER silent_mutation Average:61.541; most accessible tissue: Zhenshan97 flower, score: 79.365 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0607014877 NA 4.95E-08 mr1970 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
vg0607014877 NA 3.57E-07 mr1973 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
vg0607014877 2.46E-07 NA mr1970_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
vg0607014877 NA 1.40E-08 mr1970_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
vg0607014877 1.24E-06 NA mr1973_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
vg0607014877 NA 9.63E-09 mr1973_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