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Detailed information for vg0316513657:

Variant ID: vg0316513657 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16513657
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.67, G: 0.32, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


GAGGCGGCGGTTTTGGCAGCGGCGTGGGGCAACAATGGTGGCTTCGGCAGTTGAAGCCGGCCGGCTGGAGGAATGGGGTGAAGCTGACACATGGGGCCTT[A/G]
GGACCATGTCGGTCAGAGAGAGAGGACCCGGGGGGAAAAAGTAGACTTTTTTGCAAGGGCGGGCCGAGGGGAGGAAATCGGCCCGAGGGGAAGGAGGGAA

Reverse complement sequence

TTCCCTCCTTCCCCTCGGGCCGATTTCCTCCCCTCGGCCCGCCCTTGCAAAAAAGTCTACTTTTTCCCCCCGGGTCCTCTCTCTCTGACCGACATGGTCC[T/C]
AAGGCCCCATGTGTCAGCTTCACCCCATTCCTCCAGCCGGCCGGCTTCAACTGCCGAAGCCACCATTGTTGCCCCACGCCGCTGCCAAAACCGCCGCCTC

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 54.40% 32.20% 0.08% 13.29% NA
All Indica  2759 77.50% 17.50% 0.04% 4.97% NA
All Japonica  1512 22.80% 49.50% 0.20% 27.58% NA
Aus  269 13.80% 64.30% 0.00% 21.93% NA
Indica I  595 62.20% 37.80% 0.00% 0.00% NA
Indica II  465 92.30% 5.60% 0.22% 1.94% NA
Indica III  913 81.50% 11.50% 0.00% 7.01% NA
Indica Intermediate  786 75.60% 16.30% 0.00% 8.14% NA
Temperate Japonica  767 1.60% 55.00% 0.39% 43.02% NA
Tropical Japonica  504 61.50% 30.00% 0.00% 8.53% NA
Japonica Intermediate  241 9.10% 72.60% 0.00% 18.26% NA
VI/Aromatic  96 9.40% 86.50% 0.00% 4.17% NA
Intermediate  90 50.00% 37.80% 0.00% 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
vg0316513657 A -> DEL N N silent_mutation Average:87.667; most accessible tissue: Minghui63 young leaf, score: 99.498 N N N N
vg0316513657 A -> G LOC_Os03g29075.1 upstream_gene_variant ; 2926.0bp to feature; MODIFIER silent_mutation Average:87.667; most accessible tissue: Minghui63 young leaf, score: 99.498 N N N N
vg0316513657 A -> G LOC_Os03g29065.1 downstream_gene_variant ; 639.0bp to feature; MODIFIER silent_mutation Average:87.667; most accessible tissue: Minghui63 young leaf, score: 99.498 N N N N
vg0316513657 A -> G LOC_Os03g29065-LOC_Os03g29075 intergenic_region ; MODIFIER silent_mutation Average:87.667; most accessible tissue: Minghui63 young leaf, score: 99.498 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)
vg0316513657 A G 0.0 0.0 -0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316513657 NA 1.17E-06 mr1389 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
vg0316513657 NA 2.69E-06 mr1542 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
vg0316513657 7.48E-06 7.48E-06 mr1054_2 Jap_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
vg0316513657 1.03E-06 1.03E-06 mr1168_2 Jap_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
vg0316513657 NA 1.87E-06 mr1220_2 Jap_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
vg0316513657 NA 8.96E-06 mr1403_2 Jap_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
vg0316513657 NA 3.11E-06 mr1423_2 Jap_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
vg0316513657 NA 6.13E-06 mr1456_2 Jap_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
vg0316513657 5.84E-07 5.84E-07 mr1470_2 Jap_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
vg0316513657 4.91E-06 4.91E-06 mr1541_2 Jap_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
vg0316513657 NA 8.37E-08 mr1542_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
vg0316513657 9.17E-07 9.17E-07 mr1547_2 Jap_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
vg0316513657 6.31E-06 2.45E-06 mr1596_2 Jap_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
vg0316513657 3.82E-06 3.82E-06 mr1603_2 Jap_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
vg0316513657 1.12E-06 1.12E-06 mr1719_2 Jap_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
vg0316513657 NA 3.44E-06 mr1736_2 Jap_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
vg0316513657 NA 1.29E-06 mr1739_2 Jap_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
vg0316513657 NA 5.86E-06 mr1765_2 Jap_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
vg0316513657 NA 1.06E-06 mr1780_2 Jap_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
vg0316513657 NA 2.31E-06 mr1781_2 Jap_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
vg0316513657 NA 5.21E-06 mr1844_2 Jap_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
vg0316513657 7.91E-09 7.91E-09 mr1914_2 Jap_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
vg0316513657 3.52E-06 3.52E-06 mr1927_2 Jap_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