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Detailed information for vg0231964086:

Variant ID: vg0231964086 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 31964086
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


GGTGTCACGTGTATGTCACGTAGGATTAAAACCGCTCCAGATTGAGTTGGAGGGTAATTTGTCCGGTTTTAATAGTTTGAGGTTTAATATGTCTGTTTTT[G/A]
TGTGTGGGGGGGGTAATTCGTACTTTTTTTCTAATTTGTAAACAAATATAACATTTTCATAAGTTAACTGTCAAAATTCTAAAAGCTACACTTACGAACA

Reverse complement sequence

TGTTCGTAAGTGTAGCTTTTAGAATTTTGACAGTTAACTTATGAAAATGTTATATTTGTTTACAAATTAGAAAAAAAGTACGAATTACCCCCCCCACACA[C/T]
AAAAACAGACATATTAAACCTCAAACTATTAAAACCGGACAAATTACCCTCCAACTCAATCTGGAGCGGTTTTAATCCTACGTGACATACACGTGACACC

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 49.40% 48.70% 1.06% 0.80% NA
All Indica  2759 81.50% 17.50% 0.94% 0.00% NA
All Japonica  1512 0.50% 96.30% 0.93% 2.31% NA
Aus  269 21.90% 77.70% 0.37% 0.00% NA
Indica I  595 98.80% 1.00% 0.17% 0.00% NA
Indica II  465 65.40% 34.00% 0.65% 0.00% NA
Indica III  913 88.20% 10.60% 1.20% 0.00% NA
Indica Intermediate  786 70.20% 28.40% 1.40% 0.00% NA
Temperate Japonica  767 0.40% 98.80% 0.52% 0.26% NA
Tropical Japonica  504 0.00% 94.80% 0.79% 4.37% NA
Japonica Intermediate  241 1.70% 91.30% 2.49% 4.56% NA
VI/Aromatic  96 1.00% 89.60% 6.25% 3.12% NA
Intermediate  90 22.20% 74.40% 3.33% 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
vg0231964086 G -> A LOC_Os02g52190.1 upstream_gene_variant ; 2901.0bp to feature; MODIFIER silent_mutation Average:85.353; most accessible tissue: Zhenshan97 flag leaf, score: 95.575 N N N N
vg0231964086 G -> A LOC_Os02g52210.1 upstream_gene_variant ; 3710.0bp to feature; MODIFIER silent_mutation Average:85.353; most accessible tissue: Zhenshan97 flag leaf, score: 95.575 N N N N
vg0231964086 G -> A LOC_Os02g52210.2 upstream_gene_variant ; 3710.0bp to feature; MODIFIER silent_mutation Average:85.353; most accessible tissue: Zhenshan97 flag leaf, score: 95.575 N N N N
vg0231964086 G -> A LOC_Os02g52200.1 downstream_gene_variant ; 916.0bp to feature; MODIFIER silent_mutation Average:85.353; most accessible tissue: Zhenshan97 flag leaf, score: 95.575 N N N N
vg0231964086 G -> A LOC_Os02g52200-LOC_Os02g52210 intergenic_region ; MODIFIER silent_mutation Average:85.353; most accessible tissue: Zhenshan97 flag leaf, score: 95.575 N N N N
vg0231964086 G -> DEL N N silent_mutation Average:85.353; most accessible tissue: Zhenshan97 flag leaf, score: 95.575 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)
vg0231964086 G A -0.01 -0.01 -0.01 0.0 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0231964086 NA 1.08E-07 Grain_thickness Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0231964086 NA 2.06E-10 mr1712 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
vg0231964086 NA 1.76E-08 mr1717 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
vg0231964086 NA 2.12E-08 mr1770 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
vg0231964086 NA 7.05E-08 mr1946 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
vg0231964086 NA 7.54E-09 mr1050_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
vg0231964086 NA 6.58E-06 mr1123_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
vg0231964086 NA 2.83E-08 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
vg0231964086 NA 7.44E-06 mr1405_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
vg0231964086 NA 1.04E-08 mr1478_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
vg0231964086 NA 2.02E-13 mr1717_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
vg0231964086 NA 7.45E-12 mr1722_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
vg0231964086 NA 7.49E-08 mr1722_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
vg0231964086 NA 4.05E-11 mr1728_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
vg0231964086 NA 2.66E-14 mr1835_2 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
vg0231964086 NA 3.82E-07 mr1835_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
vg0231964086 NA 1.79E-18 mr1904_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
vg0231964086 NA 4.15E-09 mr1904_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
vg0231964086 NA 9.71E-07 mr1910_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
vg0231964086 NA 4.97E-09 mr1946_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
vg0231964086 NA 4.97E-09 mr1948_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