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Detailed information for vg0432564131:

Variant ID: vg0432564131 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32564131
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.06, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:


TAACATAGAAAAATCTTTTGGCCGTACTTTTTTCATCTGGGTCCCTATTGGGGCGGCAAGGGACCCAGATGAAAAAGTACGGCCGCAAGCTCTGAATGGG[T/C]
GGCCAAAATTGCAATTAGCCCCTTGCCGCCCTCTGTATGGGCGGCAAGGGCCTAATCGCAATTTTGGCCGACGGCGGCAGACGGCGCGGTCGACCCACCG

Reverse complement sequence

CGGTGGGTCGACCGCGCCGTCTGCCGCCGTCGGCCAAAATTGCGATTAGGCCCTTGCCGCCCATACAGAGGGCGGCAAGGGGCTAATTGCAATTTTGGCC[A/G]
CCCATTCAGAGCTTGCGGCCGTACTTTTTCATCTGGGTCCCTTGCCGCCCCAATAGGGACCCAGATGAAAAAAGTACGGCCAAAAGATTTTTCTATGTTA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.10% 5.90% 1.74% 25.31% NA
All Indica  2759 74.80% 0.60% 0.87% 23.74% NA
All Japonica  1512 64.40% 15.10% 0.46% 20.11% NA
Aus  269 19.00% 10.00% 6.69% 64.31% NA
Indica I  595 91.90% 0.20% 0.17% 7.73% NA
Indica II  465 75.90% 1.50% 0.43% 22.15% NA
Indica III  913 58.60% 0.20% 1.31% 39.87% NA
Indica Intermediate  786 79.90% 0.90% 1.15% 18.07% NA
Temperate Japonica  767 72.40% 20.70% 0.13% 6.78% NA
Tropical Japonica  504 68.70% 6.00% 0.40% 25.00% NA
Japonica Intermediate  241 29.90% 16.20% 1.66% 52.28% NA
VI/Aromatic  96 18.80% 1.00% 30.21% 50.00% NA
Intermediate  90 72.20% 5.60% 4.44% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0432564131 T -> C LOC_Os04g54759.1 intron_variant ; MODIFIER silent_mutation Average:40.801; most accessible tissue: Zhenshan97 flag leaf, score: 81.008 N N N N
vg0432564131 T -> DEL N N silent_mutation Average:40.801; most accessible tissue: Zhenshan97 flag leaf, score: 81.008 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)
vg0432564131 T C 0.02 0.01 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
vg0432564131 2.46E-06 3.20E-09 mr1800 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
vg0432564131 3.84E-06 5.07E-08 mr1800 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
vg0432564131 NA 4.06E-08 mr1544_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
vg0432564131 NA 8.76E-06 mr1638_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
vg0432564131 NA 1.87E-08 mr1740_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
vg0432564131 1.64E-07 4.02E-10 mr1741_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
vg0432564131 7.30E-06 NA mr1771_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
vg0432564131 1.02E-07 NA mr1784_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
vg0432564131 NA 8.11E-06 mr1784_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
vg0432564131 2.03E-07 6.76E-08 mr1785_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
vg0432564131 NA 2.78E-06 mr1786_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
vg0432564131 2.76E-11 1.58E-15 mr1800_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
vg0432564131 7.58E-09 2.24E-11 mr1800_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
vg0432564131 2.02E-06 NA mr1873_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