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Detailed information for vg0813433527:

Variant ID: vg0813433527 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 13433527
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


GATAATTTGGGAACATTCCTCCTGGTAGATAAACTGGTCCTGTAGCTTGATACTCGGCCATTGAACCATCAACCATTGTTTTCACGATGTTTGACAAAGT[A/G]
TTGACTAATATTCCAGACTGATTGATCAAAGCATGGTGCACGGCATAGTCAACCTGATGTTGGAAGTTGTTAAACTGTAACTGTGCCGTATTGCCATCTT

Reverse complement sequence

AAGATGGCAATACGGCACAGTTACAGTTTAACAACTTCCAACATCAGGTTGACTATGCCGTGCACCATGCTTTGATCAATCAGTCTGGAATATTAGTCAA[T/C]
ACTTTGTCAAACATCGTGAAAACAATGGTTGATGGTTCAATGGCCGAGTATCAAGCTACAGGACCAGTTTATCTACCAGGAGGAATGTTCCCAAATTATC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 47.90% 1.00% 21.84% 29.22% NA
All Indica  2759 25.00% 1.60% 30.34% 43.06% NA
All Japonica  1512 93.30% 0.10% 0.79% 5.75% NA
Aus  269 5.90% 0.40% 63.57% 30.11% NA
Indica I  595 14.50% 0.30% 22.69% 62.52% NA
Indica II  465 21.90% 1.90% 36.77% 39.35% NA
Indica III  913 35.00% 1.90% 32.09% 31.00% NA
Indica Intermediate  786 23.20% 2.00% 30.28% 44.53% NA
Temperate Japonica  767 95.20% 0.30% 0.52% 4.04% NA
Tropical Japonica  504 94.40% 0.00% 0.60% 4.96% NA
Japonica Intermediate  241 85.10% 0.00% 2.07% 12.86% NA
VI/Aromatic  96 95.80% 0.00% 0.00% 4.17% NA
Intermediate  90 63.30% 0.00% 13.33% 23.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0813433527 A -> G LOC_Os08g22284.1 synonymous_variant ; p.Asn221Asn; LOW synonymous_codon Average:10.569; most accessible tissue: Callus, score: 32.471 N N N N
vg0813433527 A -> DEL LOC_Os08g22284.1 N frameshift_variant Average:10.569; most accessible tissue: Callus, score: 32.471 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0813433527 6.11E-06 2.35E-10 mr1053 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
vg0813433527 2.48E-06 2.17E-07 mr1053 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
vg0813433527 3.34E-06 4.04E-06 mr1070 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
vg0813433527 2.85E-06 6.34E-07 mr1128 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
vg0813433527 NA 2.94E-09 mr1709 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
vg0813433527 NA 1.38E-07 mr1709 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
vg0813433527 NA 2.57E-08 mr1027_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
vg0813433527 NA 8.77E-08 mr1053_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
vg0813433527 NA 5.67E-06 mr1152_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
vg0813433527 NA 5.21E-07 mr1250_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
vg0813433527 9.73E-06 9.73E-06 mr1250_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