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Detailed information for vg1208915362:

Variant ID: vg1208915362 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 8915362
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.77, G: 0.23, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


GCAGTGACGTGACGCTTACGTGGCAATTCGATCCGGAAAAATAATAAATCCCGTGGAACCCACATGTCAGTGTCACTCATAAATTAATAAAAAATAGTGG[A/G]
CCCACATGTCATTGTCAGCTTCTCCCTCTCTTCAACTCTCTCTCTCCTCTCCCATCGGCCATCCCCATTGGCTTCCGAGCGCAGCGAATGGCGAGGAGAG

Reverse complement sequence

CTCTCCTCGCCATTCGCTGCGCTCGGAAGCCAATGGGGATGGCCGATGGGAGAGGAGAGAGAGAGTTGAAGAGAGGGAGAAGCTGACAATGACATGTGGG[T/C]
CCACTATTTTTTATTAATTTATGAGTGACACTGACATGTGGGTTCCACGGGATTTATTATTTTTCCGGATCGAATTGCCACGTAAGCGTCACGTCACTGC

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 39.90% 34.00% 0.78% 25.24% NA
All Indica  2759 54.20% 3.60% 1.23% 40.99% NA
All Japonica  1512 4.40% 94.00% 0.07% 1.52% NA
Aus  269 83.60% 7.10% 0.37% 8.92% NA
Indica I  595 34.60% 3.50% 2.35% 59.50% NA
Indica II  465 51.40% 4.50% 1.51% 42.58% NA
Indica III  913 66.30% 2.70% 0.55% 30.45% NA
Indica Intermediate  786 56.60% 4.10% 1.02% 38.30% NA
Temperate Japonica  767 5.90% 92.20% 0.13% 1.83% NA
Tropical Japonica  504 3.60% 95.40% 0.00% 0.99% NA
Japonica Intermediate  241 1.20% 97.10% 0.00% 1.66% NA
VI/Aromatic  96 72.90% 22.90% 0.00% 4.17% NA
Intermediate  90 34.40% 52.20% 1.11% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1208915362 A -> DEL N N silent_mutation Average:57.033; most accessible tissue: Minghui63 young leaf, score: 90.886 N N N N
vg1208915362 A -> G LOC_Os12g15590.1 upstream_gene_variant ; 386.0bp to feature; MODIFIER silent_mutation Average:57.033; most accessible tissue: Minghui63 young leaf, score: 90.886 N N N N
vg1208915362 A -> G LOC_Os12g15620.1 upstream_gene_variant ; 4314.0bp to feature; MODIFIER silent_mutation Average:57.033; most accessible tissue: Minghui63 young leaf, score: 90.886 N N N N
vg1208915362 A -> G LOC_Os12g15590.2 upstream_gene_variant ; 256.0bp to feature; MODIFIER silent_mutation Average:57.033; most accessible tissue: Minghui63 young leaf, score: 90.886 N N N N
vg1208915362 A -> G LOC_Os12g15600.1 downstream_gene_variant ; 203.0bp to feature; MODIFIER silent_mutation Average:57.033; most accessible tissue: Minghui63 young leaf, score: 90.886 N N N N
vg1208915362 A -> G LOC_Os12g15610.1 downstream_gene_variant ; 2959.0bp to feature; MODIFIER silent_mutation Average:57.033; most accessible tissue: Minghui63 young leaf, score: 90.886 N N N N
vg1208915362 A -> G LOC_Os12g15590-LOC_Os12g15600 intergenic_region ; MODIFIER silent_mutation Average:57.033; most accessible tissue: Minghui63 young leaf, score: 90.886 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)
vg1208915362 A G 0.11 0.13 0.09 0.12 0.1 0.1

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1208915362 NA 3.21E-34 mr1350 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
vg1208915362 NA 2.76E-18 mr1529 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
vg1208915362 NA 3.19E-06 mr1020_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
vg1208915362 NA 1.10E-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
vg1208915362 NA 5.21E-31 mr1105_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
vg1208915362 NA 7.16E-15 mr1133_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
vg1208915362 NA 2.93E-17 mr1146_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
vg1208915362 NA 6.44E-33 mr1256_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
vg1208915362 NA 1.48E-06 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
vg1208915362 NA 2.93E-22 mr1298_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
vg1208915362 NA 7.99E-25 mr1350_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
vg1208915362 NA 2.85E-35 mr1448_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
vg1208915362 NA 1.51E-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
vg1208915362 NA 1.14E-14 mr1529_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
vg1208915362 NA 2.73E-47 mr1546_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
vg1208915362 NA 1.02E-13 mr1575_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
vg1208915362 NA 1.07E-10 mr1667_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
vg1208915362 NA 4.11E-21 mr1698_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
vg1208915362 NA 3.33E-17 mr1712_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
vg1208915362 NA 2.01E-11 mr1714_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
vg1208915362 NA 1.05E-12 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
vg1208915362 NA 4.03E-21 mr1731_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
vg1208915362 6.00E-07 NA mr1750_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
vg1208915362 NA 1.53E-69 mr1889_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
vg1208915362 NA 2.51E-66 mr1896_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
vg1208915362 NA 1.15E-12 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
vg1208915362 NA 3.34E-96 mr1907_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
vg1208915362 NA 1.93E-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
vg1208915362 NA 9.16E-20 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
vg1208915362 NA 2.75E-86 mr1934_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