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Detailed information for vg0628632216:

Variant ID: vg0628632216 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 28632216
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.83, C: 0.16, others allele: 0.00, population size: 36. )

Flanking Sequence (100 bp) in Reference Genome:


TTATCTGTAATTTATCGTATCTATTCAGATCATACAGCATTGTCAGATCCATGATTTATTATGTTTACCTAGAGCATATTTTTTATACAATATCTATTGT[G/C]
CAAGTGTCCCCGATGTTAAATCGACTACGCTTTAACGTTGGGGGCTCGCTCTATTTTCTTCTGTATGAATCATGCTTGCTTACGGTTTACATAATGCCTG

Reverse complement sequence

CAGGCATTATGTAAACCGTAAGCAAGCATGATTCATACAGAAGAAAATAGAGCGAGCCCCCAACGTTAAAGCGTAGTCGATTTAACATCGGGGACACTTG[C/G]
ACAATAGATATTGTATAAAAAATATGCTCTAGGTAAACATAATAAATCATGGATCTGACAATGCTGTATGATCTGAATAGATACGATAAATTACAGATAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.50% 35.40% 0.06% 0.00% NA
All Indica  2759 41.70% 58.20% 0.07% 0.00% NA
All Japonica  1512 98.40% 1.60% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 58.30% 41.70% 0.00% 0.00% NA
Indica II  465 15.70% 84.30% 0.00% 0.00% NA
Indica III  913 44.10% 55.80% 0.11% 0.00% NA
Indica Intermediate  786 41.60% 58.30% 0.13% 0.00% NA
Temperate Japonica  767 97.10% 2.90% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 7.30% 1.04% 0.00% NA
Intermediate  90 61.10% 38.90% 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
vg0628632216 G -> C LOC_Os06g47220.1 upstream_gene_variant ; 2307.0bp to feature; MODIFIER silent_mutation Average:44.598; most accessible tissue: Minghui63 flower, score: 55.591 N N N N
vg0628632216 G -> C LOC_Os06g47210.1 downstream_gene_variant ; 4210.0bp to feature; MODIFIER silent_mutation Average:44.598; most accessible tissue: Minghui63 flower, score: 55.591 N N N N
vg0628632216 G -> C LOC_Os06g47220-LOC_Os06g47230 intergenic_region ; MODIFIER silent_mutation Average:44.598; most accessible tissue: Minghui63 flower, score: 55.591 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0628632216 1.69E-06 3.02E-06 mr1216 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
vg0628632216 NA 6.09E-07 mr1321_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
vg0628632216 NA 2.84E-08 mr1974_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
vg0628632216 NA 2.13E-07 mr1974_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