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Detailed information for vg1114515282:

Variant ID: vg1114515282 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 14515282
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.84, A: 0.15, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


ATTATAGGGGTGGAAAGTTTTGGTGTGTCACATCGCATATACATGAATACACAATTAAAGTATTAAACGTAGTCTAATAACAAAATAAATTGCAGATTTT[A/G]
TCTGTAAACTGCGAGACGAATTTATTATGTCTAATTAATCTGTCATTAGCAAATGATTACTGTAACACCACATTGTCAAATCATGACGCAATTAAACTTA

Reverse complement sequence

TAAGTTTAATTGCGTCATGATTTGACAATGTGGTGTTACAGTAATCATTTGCTAATGACAGATTAATTAGACATAATAAATTCGTCTCGCAGTTTACAGA[T/C]
AAAATCTGCAATTTATTTTGTTATTAGACTACGTTTAATACTTTAATTGTGTATTCATGTATATGCGATGTGACACACCAAAACTTTCCACCCCTATAAT

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 60.20% 39.60% 0.21% 0.00% NA
All Indica  2759 89.30% 10.40% 0.25% 0.00% NA
All Japonica  1512 3.30% 96.60% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 90.40% 9.20% 0.34% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 84.40% 15.40% 0.11% 0.00% NA
Indica Intermediate  786 89.20% 10.30% 0.51% 0.00% NA
Temperate Japonica  767 3.70% 96.30% 0.00% 0.00% NA
Tropical Japonica  504 3.40% 96.40% 0.20% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 9.40% 90.60% 0.00% 0.00% NA
Intermediate  90 56.70% 41.10% 2.22% 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
vg1114515282 A -> G LOC_Os11g25480.1 upstream_gene_variant ; 4097.0bp to feature; MODIFIER silent_mutation Average:72.195; most accessible tissue: Minghui63 root, score: 97.388 N N N N
vg1114515282 A -> G LOC_Os11g25470.1 downstream_gene_variant ; 1631.0bp to feature; MODIFIER silent_mutation Average:72.195; most accessible tissue: Minghui63 root, score: 97.388 N N N N
vg1114515282 A -> G LOC_Os11g25454.1 intron_variant ; MODIFIER silent_mutation Average:72.195; most accessible tissue: Minghui63 root, score: 97.388 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg1114515282 A G 0.04 0.01 0.0 -0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1114515282 NA 2.52E-09 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
vg1114515282 NA 2.74E-21 mr1168 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
vg1114515282 NA 7.81E-23 mr1375 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
vg1114515282 NA 2.25E-23 mr1383 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
vg1114515282 NA 3.32E-91 mr1758 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
vg1114515282 2.94E-08 1.83E-135 mr1758_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
vg1114515282 3.36E-08 4.98E-10 mr1758_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