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Detailed information for vg0410688931:

Variant ID: vg0410688931 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 10688931
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

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:


TTGGCATCAAGGATTGTAACCTGTCAGCAAAAACCTTGCACAGGATTTTAACAGAGAAGTTCATCAATGAGATTGGTCTATAATCATTGGGGGTTTGAGG[A/T]
CTTGGTTTCTTTGGGACCAAGGTGATATACGAAAAATTGATAGAAGACAAATCCACCGAGTTTCCCCAAAATACAAGGGGACTTGGTCAAGCCCGAATGA

Reverse complement sequence

TCATTCGGGCTTGACCAAGTCCCCTTGTATTTTGGGGAAACTCGGTGGATTTGTCTTCTATCAATTTTTCGTATATCACCTTGGTCCCAAAGAAACCAAG[T/A]
CCTCAAACCCCCAATGATTATAGACCAATCTCATTGATGAACTTCTCTGTTAAAATCCTGTGCAAGGTTTTTGCTGACAGGTTACAATCCTTGATGCCAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.30% 1.90% 1.80% 12.97% NA
All Indica  2759 99.60% 0.00% 0.07% 0.29% NA
All Japonica  1512 54.20% 6.00% 4.70% 35.05% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.90% 0.00% 0.22% 0.86% NA
Indica III  913 99.80% 0.00% 0.00% 0.22% NA
Indica Intermediate  786 99.60% 0.00% 0.13% 0.25% NA
Temperate Japonica  767 80.10% 10.70% 6.13% 3.13% NA
Tropical Japonica  504 7.50% 1.40% 3.57% 87.50% NA
Japonica Intermediate  241 69.70% 0.80% 2.49% 26.97% NA
VI/Aromatic  96 30.20% 0.00% 9.38% 60.42% NA
Intermediate  90 77.80% 0.00% 3.33% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0410688931 A -> DEL N N silent_mutation Average:38.945; most accessible tissue: Callus, score: 57.588 N N N N
vg0410688931 A -> T LOC_Os04g19250.1 upstream_gene_variant ; 295.0bp to feature; MODIFIER silent_mutation Average:38.945; most accessible tissue: Callus, score: 57.588 N N N N
vg0410688931 A -> T LOC_Os04g19240.1 downstream_gene_variant ; 2529.0bp to feature; MODIFIER silent_mutation Average:38.945; most accessible tissue: Callus, score: 57.588 N N N N
vg0410688931 A -> T LOC_Os04g19240-LOC_Os04g19250 intergenic_region ; MODIFIER silent_mutation Average:38.945; most accessible tissue: Callus, score: 57.588 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0410688931 6.97E-07 9.39E-08 mr1035 Jap_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
vg0410688931 2.67E-07 7.81E-13 mr1062 Jap_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
vg0410688931 4.00E-07 4.00E-07 mr1525 Jap_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
vg0410688931 2.57E-06 4.96E-07 mr1626 Jap_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
vg0410688931 4.00E-09 9.95E-13 mr1062_2 Jap_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
vg0410688931 5.20E-06 5.20E-06 mr1525_2 Jap_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
vg0410688931 4.31E-07 1.36E-10 mr1631_2 Jap_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