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Detailed information for vg1125555062:

Variant ID: vg1125555062 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25555062
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.72, A: 0.28, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


TGTCTGTAGGCATCATGTAGTTGTACATAGGCCGTGATTAGATTTAAATTTTTTTCTTCGAACTTCCAACTTTTCCGTGACATCAAATGCTTAGACACAT[A/G]
TATGGAGCATTAAATATAGACAAAAAAAAACCAATTGTACAGTTTGCATGTAAATCGCAAGATGAATCTTTTGAGTCTAATTACGCCATGATTTGACAAT

Reverse complement sequence

ATTGTCAAATCATGGCGTAATTAGACTCAAAAGATTCATCTTGCGATTTACATGCAAACTGTACAATTGGTTTTTTTTTGTCTATATTTAATGCTCCATA[T/C]
ATGTGTCTAAGCATTTGATGTCACGGAAAAGTTGGAAGTTCGAAGAAAAAAATTTAAATCTAATCACGGCCTATGTACAACTACATGATGCCTACAGACA

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 42.40% 33.20% 0.40% 23.93% NA
All Indica  2759 30.50% 34.60% 0.62% 34.29% NA
All Japonica  1512 68.30% 24.40% 0.07% 7.28% NA
Aus  269 21.90% 58.70% 0.00% 19.33% NA
Indica I  595 51.10% 36.60% 0.17% 12.10% NA
Indica II  465 57.40% 37.20% 0.43% 4.95% NA
Indica III  913 3.50% 37.10% 0.66% 58.71% NA
Indica Intermediate  786 30.30% 28.60% 1.02% 40.08% NA
Temperate Japonica  767 62.70% 35.10% 0.13% 2.09% NA
Tropical Japonica  504 72.60% 11.90% 0.00% 15.48% NA
Japonica Intermediate  241 76.80% 16.60% 0.00% 6.64% NA
VI/Aromatic  96 43.80% 56.20% 0.00% 0.00% NA
Intermediate  90 35.60% 37.80% 1.11% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1125555062 A -> DEL N N silent_mutation Average:54.327; most accessible tissue: Zhenshan97 panicle, score: 86.788 N N N N
vg1125555062 A -> G LOC_Os11g42450.1 downstream_gene_variant ; 1507.0bp to feature; MODIFIER silent_mutation Average:54.327; most accessible tissue: Zhenshan97 panicle, score: 86.788 N N N N
vg1125555062 A -> G LOC_Os11g42450-LOC_Os11g42470 intergenic_region ; MODIFIER silent_mutation Average:54.327; most accessible tissue: Zhenshan97 panicle, score: 86.788 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)
vg1125555062 A G 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125555062 6.18E-07 NA mr1133 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
vg1125555062 1.11E-10 7.18E-17 mr1133 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
vg1125555062 2.71E-14 2.05E-24 mr1191 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
vg1125555062 2.44E-17 2.18E-20 mr1191 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
vg1125555062 NA 8.54E-06 mr1561 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
vg1125555062 1.58E-17 1.18E-31 mr1644 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
vg1125555062 1.00E-22 1.89E-27 mr1644 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
vg1125555062 1.08E-06 NA mr1667 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
vg1125555062 2.29E-07 1.44E-10 mr1667 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
vg1125555062 NA 9.32E-06 mr1908 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
vg1125555062 3.94E-06 3.14E-12 mr1133_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
vg1125555062 7.48E-17 2.01E-33 mr1191_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
vg1125555062 2.58E-21 9.28E-28 mr1191_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
vg1125555062 NA 1.76E-06 mr1380_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
vg1125555062 NA 2.40E-06 mr1561_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
vg1125555062 NA 2.08E-08 mr1667_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
vg1125555062 NA 3.43E-06 mr1996_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