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Detailed information for vg0802211662:

Variant ID: vg0802211662 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 2211662
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.79, G: 0.22, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


GGATTTCATGGTGGTCAGTACTTTCTTGTAGAAGAACTTCATGTAGCCTGGAAGTTCTTCAGCGGCTTCCTCATCCCATCTATTATATTTTTATGGTTCA[A/G]
TCATTGATAAAAATTAAATTCAAGTTAAAGACAAGAATTTTGGCTCCATGCAGCTTCTTTGAAACAAATTAAGTTCGGAATGAATTTCATTATTAAAAGA

Reverse complement sequence

TCTTTTAATAATGAAATTCATTCCGAACTTAATTTGTTTCAAAGAAGCTGCATGGAGCCAAAATTCTTGTCTTTAACTTGAATTTAATTTTTATCAATGA[T/C]
TGAACCATAAAAATATAATAGATGGGATGAGGAAGCCGCTGAAGAACTTCCAGGCTACATGAAGTTCTTCTACAAGAAAGTACTGACCACCATGAAATCC

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 58.30% 41.30% 0.15% 0.30% NA
All Indica  2759 34.10% 65.20% 0.18% 0.47% NA
All Japonica  1512 98.40% 1.60% 0.00% 0.00% NA
Aus  269 65.40% 34.60% 0.00% 0.00% NA
Indica I  595 39.50% 60.20% 0.00% 0.34% NA
Indica II  465 15.50% 83.90% 0.43% 0.22% NA
Indica III  913 31.10% 68.30% 0.33% 0.22% NA
Indica Intermediate  786 44.50% 54.50% 0.00% 1.02% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 61.10% 35.60% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0802211662 A -> G LOC_Os08g04490.1 downstream_gene_variant ; 1973.0bp to feature; MODIFIER silent_mutation Average:47.005; most accessible tissue: Zhenshan97 young leaf, score: 59.009 N N N N
vg0802211662 A -> G LOC_Os08g04500.1 intron_variant ; MODIFIER silent_mutation Average:47.005; most accessible tissue: Zhenshan97 young leaf, score: 59.009 N N N N
vg0802211662 A -> G LOC_Os08g04500.2 intron_variant ; MODIFIER silent_mutation Average:47.005; most accessible tissue: Zhenshan97 young leaf, score: 59.009 N N N N
vg0802211662 A -> DEL N N silent_mutation Average:47.005; most accessible tissue: Zhenshan97 young leaf, score: 59.009 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0802211662 NA 3.65E-07 mr1593 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
vg0802211662 1.49E-33 3.26E-31 mr1739 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
vg0802211662 9.72E-37 1.13E-65 mr1739 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
vg0802211662 NA 1.10E-06 mr1268_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
vg0802211662 1.94E-29 8.05E-27 mr1739_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
vg0802211662 1.79E-43 6.86E-76 mr1739_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