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Detailed information for vg1115487625:

Variant ID: vg1115487625 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 15487625
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.02, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


GGGACAAGTGGGTGGGTCCAACAGATGAGCACGTGGGGGAGGGGGAGGGACCGATTTTCCCACCTCCCCCGGTCAACCGATGCTGGGCATTCTCCTATAT[T/A]
AAGGGCACGGCTAAATCAATAATTAGCACACATTTAATGGGCCGGGTCAATGTTTGCTTGGCAAATCCAATATTACTATAAAGTTGATGCTCGCTACTTG

Reverse complement sequence

CAAGTAGCGAGCATCAACTTTATAGTAATATTGGATTTGCCAAGCAAACATTGACCCGGCCCATTAAATGTGTGCTAATTATTGATTTAGCCGTGCCCTT[A/T]
ATATAGGAGAATGCCCAGCATCGGTTGACCGGGGGAGGTGGGAAAATCGGTCCCTCCCCCTCCCCCACGTGCTCATCTGTTGGACCCACCCACTTGTCCC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.30% 30.40% 0.25% 0.00% NA
All Indica  2759 52.70% 46.80% 0.43% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 60.20% 39.80% 0.00% 0.00% NA
Indica I  595 23.20% 76.50% 0.34% 0.00% NA
Indica II  465 63.00% 36.30% 0.65% 0.00% NA
Indica III  913 61.20% 38.40% 0.33% 0.00% NA
Indica Intermediate  786 59.20% 40.30% 0.51% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 72.20% 27.80% 0.00% 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
vg1115487625 T -> A LOC_Os11g26930.1 downstream_gene_variant ; 397.0bp to feature; MODIFIER silent_mutation Average:68.316; most accessible tissue: Zhenshan97 root, score: 78.34 N N N N
vg1115487625 T -> A LOC_Os11g26940.1 downstream_gene_variant ; 4063.0bp to feature; MODIFIER silent_mutation Average:68.316; most accessible tissue: Zhenshan97 root, score: 78.34 N N N N
vg1115487625 T -> A LOC_Os11g26930-LOC_Os11g26940 intergenic_region ; MODIFIER silent_mutation Average:68.316; most accessible tissue: Zhenshan97 root, score: 78.34 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1115487625 NA 2.81E-06 mr1077 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
vg1115487625 NA 4.02E-12 mr1097 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
vg1115487625 NA 1.73E-07 mr1097 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
vg1115487625 NA 2.29E-06 mr1149 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
vg1115487625 NA 6.00E-07 mr1154 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
vg1115487625 NA 6.48E-07 mr1861 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
vg1115487625 NA 8.21E-08 mr1092_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
vg1115487625 1.95E-08 3.71E-17 mr1097_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
vg1115487625 1.02E-07 6.65E-12 mr1097_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
vg1115487625 1.11E-07 NA mr1102_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
vg1115487625 9.37E-06 2.99E-07 mr1102_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
vg1115487625 NA 1.03E-07 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
vg1115487625 7.31E-09 NA mr1154_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
vg1115487625 6.00E-09 9.61E-15 mr1154_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
vg1115487625 1.96E-07 NA mr1223_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
vg1115487625 NA 1.85E-06 mr1223_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