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Detailed information for vg0629695392:

Variant ID: vg0629695392 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 29695392
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTTGCATGATGTTTAAATGTGATGATTGTTAGTGGATAATGATGTGGCATCTTGTTAATTAGTGGATGATGATGTGGCATCTTTGCATGTTAAGCTTAA[G/C]
GAGTTAGTGGGGGATAACTTTATAGTAAGATAGGATTCAATTATTCAACAAACACCATCGATAACACCAAAACCACATCATGCATCAAAAAAACCTTTGC

Reverse complement sequence

GCAAAGGTTTTTTTGATGCATGATGTGGTTTTGGTGTTATCGATGGTGTTTGTTGAATAATTGAATCCTATCTTACTATAAAGTTATCCCCCACTAACTC[C/G]
TTAAGCTTAACATGCAAAGATGCCACATCATCATCCACTAATTAACAAGATGCCACATCATTATCCACTAACAATCATCACATTTAAACATCATGCAAAC

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 96.80% 3.00% 0.19% 0.00% NA
All Indica  2759 99.80% 0.10% 0.07% 0.00% NA
All Japonica  1512 90.50% 9.10% 0.46% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.40% 0.25% 0.00% NA
Temperate Japonica  767 81.70% 17.30% 0.91% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0629695392 G -> C LOC_Os06g49000.1 upstream_gene_variant ; 1188.0bp to feature; MODIFIER silent_mutation Average:23.996; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N
vg0629695392 G -> C LOC_Os06g49000.2 upstream_gene_variant ; 1168.0bp to feature; MODIFIER silent_mutation Average:23.996; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N
vg0629695392 G -> C LOC_Os06g48990-LOC_Os06g49000 intergenic_region ; MODIFIER silent_mutation Average:23.996; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0629695392 NA 8.00E-08 mr1648 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
vg0629695392 NA 1.59E-07 mr1164_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
vg0629695392 NA 9.67E-08 mr1296_2 Jap_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
vg0629695392 NA 1.18E-06 mr1358_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
vg0629695392 NA 2.28E-06 mr1631_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
vg0629695392 NA 7.75E-07 mr1875_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