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Detailed information for vg1219658723:

Variant ID: vg1219658723 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 19658723
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


CCCCAAAAGAACATACATTTCTTCTAGTTTATCATTCTCATCCCTTTGCTATATGTTTTCCTGCTTCACTTGTTCCTTGCTTCAGCTCTAACCCAGGGGC[A/G]
GATCCACTGTATAGGCAGTGGGGTCCCAGGACCCCAGTCAAATTTTAATGTATGACATATGGGCCCCCACTACACCCGGGAAAAAGGACCCCACTCTCAT

Reverse complement sequence

ATGAGAGTGGGGTCCTTTTTCCCGGGTGTAGTGGGGGCCCATATGTCATACATTAAAATTTGACTGGGGTCCTGGGACCCCACTGCCTATACAGTGGATC[T/C]
GCCCCTGGGTTAGAGCTGAAGCAAGGAACAAGTGAAGCAGGAAAACATATAGCAAAGGGATGAGAATGATAAACTAGAAGAAATGTATGTTCTTTTGGGG

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 64.70% 32.40% 0.08% 2.77% NA
All Indica  2759 92.20% 3.10% 0.11% 4.64% NA
All Japonica  1512 13.20% 86.80% 0.00% 0.07% NA
Aus  269 97.00% 2.60% 0.37% 0.00% NA
Indica I  595 96.60% 2.40% 0.00% 1.01% NA
Indica II  465 80.60% 2.20% 0.22% 16.99% NA
Indica III  913 96.60% 1.40% 0.11% 1.86% NA
Indica Intermediate  786 90.50% 6.10% 0.13% 3.31% NA
Temperate Japonica  767 17.60% 82.40% 0.00% 0.00% NA
Tropical Japonica  504 3.80% 96.20% 0.00% 0.00% NA
Japonica Intermediate  241 18.70% 80.90% 0.00% 0.41% NA
VI/Aromatic  96 21.90% 78.10% 0.00% 0.00% NA
Intermediate  90 38.90% 58.90% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1219658723 A -> DEL N N silent_mutation Average:64.432; most accessible tissue: Zhenshan97 flag leaf, score: 77.203 N N N N
vg1219658723 A -> G LOC_Os12g32590.1 upstream_gene_variant ; 4384.0bp to feature; MODIFIER silent_mutation Average:64.432; most accessible tissue: Zhenshan97 flag leaf, score: 77.203 N N N N
vg1219658723 A -> G LOC_Os12g32560.1 downstream_gene_variant ; 5000.0bp to feature; MODIFIER silent_mutation Average:64.432; most accessible tissue: Zhenshan97 flag leaf, score: 77.203 N N N N
vg1219658723 A -> G LOC_Os12g32580.1 intron_variant ; MODIFIER silent_mutation Average:64.432; most accessible tissue: Zhenshan97 flag leaf, score: 77.203 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)
vg1219658723 A G 0.0 0.01 0.01 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1219658723 NA 1.10E-44 mr1092 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
vg1219658723 NA 4.71E-10 mr1128 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
vg1219658723 9.01E-06 NA mr1132 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
vg1219658723 5.49E-06 NA mr1142 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
vg1219658723 NA 1.05E-43 mr1152 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
vg1219658723 1.80E-06 NA mr1489 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
vg1219658723 NA 1.55E-12 mr1940 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
vg1219658723 NA 1.23E-25 mr1024_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
vg1219658723 NA 1.24E-09 mr1084_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
vg1219658723 NA 2.30E-13 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
vg1219658723 NA 3.77E-13 mr1128_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
vg1219658723 NA 7.58E-15 mr1148_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
vg1219658723 NA 7.64E-39 mr1152_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
vg1219658723 NA 4.61E-09 mr1198_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
vg1219658723 NA 3.91E-09 mr1205_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
vg1219658723 NA 2.05E-06 mr1227_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
vg1219658723 NA 3.37E-20 mr1239_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
vg1219658723 NA 2.53E-07 mr1272_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
vg1219658723 NA 8.04E-08 mr1275_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
vg1219658723 NA 5.40E-10 mr1506_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
vg1219658723 NA 3.23E-08 mr1668_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
vg1219658723 NA 5.01E-10 mr1681_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
vg1219658723 NA 5.75E-12 mr1781_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
vg1219658723 NA 2.69E-10 mr1806_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
vg1219658723 5.50E-06 NA mr1915_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
vg1219658723 NA 1.28E-07 mr1921_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
vg1219658723 NA 1.38E-21 mr1922_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
vg1219658723 NA 7.07E-10 mr1940_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