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Detailed information for vg0824769690:

Variant ID: vg0824769690 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 24769690
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: 300. )

Flanking Sequence (100 bp) in Reference Genome:


ACCAACTGCCAGCTATGTAGATGCCATTACCACCAGTCTCATTACTAAAAAAAATCTACATATAGAGTTGATGGCATGAGTACAAGGTAATTAGGGAGTG[A/G]
TTGTCACCTTGAGAGGAATTCTTTATCTTGATGCATCCCCCTTCCATCAAGGGATTGCCGTAAGTCCCATCAGGACAGCGGCAATGAAATGTTCCGGGCA

Reverse complement sequence

TGCCCGGAACATTTCATTGCCGCTGTCCTGATGGGACTTACGGCAATCCCTTGATGGAAGGGGGATGCATCAAGATAAAGAATTCCTCTCAAGGTGACAA[T/C]
CACTCCCTAATTACCTTGTACTCATGCCATCAACTCTATATGTAGATTTTTTTTAGTAATGAGACTGGTGGTAATGGCATCTACATAGCTGGCAGTTGGT

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 85.90% 13.00% 1.10% 0.00% NA
All Indica  2759 76.60% 21.60% 1.85% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 64.70% 29.20% 6.05% 0.00% NA
Indica II  465 48.60% 50.10% 1.29% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 74.90% 23.90% 1.15% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 15.60% 1.11% 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
vg0824769690 A -> G LOC_Os08g39220.1 upstream_gene_variant ; 3271.0bp to feature; MODIFIER silent_mutation Average:45.783; most accessible tissue: Callus, score: 81.316 N N N N
vg0824769690 A -> G LOC_Os08g39210.1 intron_variant ; MODIFIER silent_mutation Average:45.783; most accessible tissue: Callus, score: 81.316 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0824769690 NA 3.19E-06 mr1212 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
vg0824769690 5.06E-06 6.55E-08 mr1699 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
vg0824769690 NA 1.41E-06 mr1727 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
vg0824769690 NA 7.01E-06 mr1874 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
vg0824769690 1.74E-06 NA mr1699_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
vg0824769690 1.24E-06 4.30E-10 mr1699_2 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
vg0824769690 NA 5.25E-10 mr1874_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