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Detailed information for vg0624160667:

Variant ID: vg0624160667 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 24160667
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.79, A: 0.21, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


TCTCTCTCTATCCCAATCTCTCTCTCTCTCTTCTCCCTCCTCTCACCAGCTCACTAGCACGGCGGCACGGAGAAGGACAACAGAGGAGTGGAGGATGACG[A/G]
CGGGCAGGATCAGAGCCAATTGAAGGTGGTGGAGGGGGACCGAGGATGGCAGTGAGCGAGGGCGGGGAAGCAGAGCTCTCTCGGGCACTGACGGTGGCAG

Reverse complement sequence

CTGCCACCGTCAGTGCCCGAGAGAGCTCTGCTTCCCCGCCCTCGCTCACTGCCATCCTCGGTCCCCCTCCACCACCTTCAATTGGCTCTGATCCTGCCCG[T/C]
CGTCATCCTCCACTCCTCTGTTGTCCTTCTCCGTGCCGCCGTGCTAGTGAGCTGGTGAGAGGAGGGAGAAGAGAGAGAGAGAGATTGGGATAGAGAGAGA

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 57.20% 42.80% 0.00% 0.00% NA
All Indica  2759 86.00% 14.00% 0.00% 0.00% NA
All Japonica  1512 13.30% 86.70% 0.00% 0.00% NA
Aus  269 3.30% 96.70% 0.00% 0.00% NA
Indica I  595 94.60% 5.40% 0.00% 0.00% NA
Indica II  465 89.70% 10.30% 0.00% 0.00% NA
Indica III  913 80.00% 20.00% 0.00% 0.00% NA
Indica Intermediate  786 84.20% 15.80% 0.00% 0.00% NA
Temperate Japonica  767 2.10% 97.90% 0.00% 0.00% NA
Tropical Japonica  504 33.50% 66.50% 0.00% 0.00% NA
Japonica Intermediate  241 6.60% 93.40% 0.00% 0.00% NA
VI/Aromatic  96 77.10% 22.90% 0.00% 0.00% NA
Intermediate  90 52.20% 47.80% 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
vg0624160667 A -> G LOC_Os06g40530.1 upstream_gene_variant ; 956.0bp to feature; MODIFIER silent_mutation Average:70.805; most accessible tissue: Zhenshan97 panicle, score: 82.336 N N N N
vg0624160667 A -> G LOC_Os06g40540.1 upstream_gene_variant ; 4448.0bp to feature; MODIFIER silent_mutation Average:70.805; most accessible tissue: Zhenshan97 panicle, score: 82.336 N N N N
vg0624160667 A -> G LOC_Os06g40530-LOC_Os06g40540 intergenic_region ; MODIFIER silent_mutation Average:70.805; most accessible tissue: Zhenshan97 panicle, score: 82.336 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0624160667 NA 2.77E-18 mr1253 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
vg0624160667 NA 3.36E-06 mr1676 Jap_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
vg0624160667 NA 8.34E-20 mr1807 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
vg0624160667 NA 6.13E-07 mr1498_2 Jap_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
vg0624160667 NA 2.13E-20 mr1807_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
vg0624160667 NA 9.60E-07 mr1807_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