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Detailed information for vg0313064084:

Variant ID: vg0313064084 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 13064084
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.78, A: 0.22, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


GACATCACCGACACTTCTATTTGCTCTTTGAAACTTGGTACGTAGTTATGATGGAACCATTCTGCCTCCTGGAGATAATACCCAGATAACAATTGAAACT[G/A]
CATAGGAGAAAACAGAACAATGCTAAGATCTATGAGGTAGGGGTGTGTGTGTATCACATAGTAAGTGCATGCTGATACTACCTCTGTTCTTTACTTGTCC

Reverse complement sequence

GGACAAGTAAAGAACAGAGGTAGTATCAGCATGCACTTACTATGTGATACACACACACCCCTACCTCATAGATCTTAGCATTGTTCTGTTTTCTCCTATG[C/T]
AGTTTCAATTGTTATCTGGGTATTATCTCCAGGAGGCAGAATGGTTCCATCATAACTACGTACCAAGTTTCAAAGAGCAAATAGAAGTGTCGGTGATGTC

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 89.90% 9.90% 0.17% 0.00% NA
All Indica  2759 87.70% 12.00% 0.25% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 51.70% 48.00% 0.37% 0.00% NA
Indica I  595 92.40% 7.40% 0.17% 0.00% NA
Indica II  465 93.10% 6.70% 0.22% 0.00% NA
Indica III  913 82.30% 17.70% 0.00% 0.00% NA
Indica Intermediate  786 87.30% 12.10% 0.64% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0313064084 G -> A LOC_Os03g22634.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:62.482; most accessible tissue: Callus, score: 81.385 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0313064084 NA 1.52E-07 mr1004 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
vg0313064084 3.52E-06 3.52E-06 mr1275 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
vg0313064084 1.55E-06 1.55E-06 mr1302 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
vg0313064084 NA 2.16E-06 mr1574 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
vg0313064084 3.11E-06 NA mr1775 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