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Detailed information for vg0410077726:

Variant ID: vg0410077726 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 10077726
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


GTCCCGATCTTCCGATAGGTTTTGATAAACAGTCGATTTGGACGGAGTCGCGACACAACTCGATCCGTTCTGAACGAACACGCTACTGAGCCCCGCAATC[G/A]
CAGCACCACGTCTCCTTTGGTTATCAACCATGCCGAAACCTGGTTGACCTCGTCGAGAAGGCTAATCCCTGCATATGAATCGAAGAACACAAGCAAGAAC

Reverse complement sequence

GTTCTTGCTTGTGTTCTTCGATTCATATGCAGGGATTAGCCTTCTCGACGAGGTCAACCAGGTTTCGGCATGGTTGATAACCAAAGGAGACGTGGTGCTG[C/T]
GATTGCGGGGCTCAGTAGCGTGTTCGTTCAGAACGGATCGAGTTGTGTCGCGACTCCGTCCAAATCGACTGTTTATCAAAACCTATCGGAAGATCGGGAC

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 96.80% 2.00% 1.23% 0.00% NA
All Indica  2759 94.70% 3.30% 1.96% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.07% 0.00% NA
Aus  269 99.30% 0.00% 0.74% 0.00% NA
Indica I  595 88.40% 7.10% 4.54% 0.00% NA
Indica II  465 97.00% 1.70% 1.29% 0.00% NA
Indica III  913 97.70% 2.30% 0.00% 0.00% NA
Indica Intermediate  786 94.70% 2.70% 2.67% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 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
vg0410077726 G -> A LOC_Os04g18230.1 downstream_gene_variant ; 1335.0bp to feature; MODIFIER silent_mutation Average:46.811; most accessible tissue: Zhenshan97 flag leaf, score: 60.074 N N N N
vg0410077726 G -> A LOC_Os04g18200-LOC_Os04g18230 intergenic_region ; MODIFIER silent_mutation Average:46.811; most accessible tissue: Zhenshan97 flag leaf, score: 60.074 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0410077726 NA 3.88E-06 mr1060 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
vg0410077726 NA 9.90E-06 mr1937 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
vg0410077726 7.64E-10 5.04E-09 mr1946 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