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Detailed information for vg0330783477:

Variant ID: vg0330783477 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 30783477
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, A: 0.03, T: 0.01, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


ATGAGAATCAAAATCTCAGCAGAATCAGGACCTGATTGTGGCTCTGTTAGCTGCTGGAGGTTCCCAATCGTGGAATAGTGCACGTGGAAATAGAGCAGTC[C/T]
ATTAGCGCGTGATTAATTAAGTATTAGCTTTTTTCCAAAATGGATCAATATAATTTTTTAAGCAACTTTTATATATATGCTTTATGAAAAAAAAACACAC

Reverse complement sequence

GTGTGTTTTTTTTTCATAAAGCATATATATAAAAGTTGCTTAAAAAATTATATTGATCCATTTTGGAAAAAAGCTAATACTTAATTAATCACGCGCTAAT[G/A]
GACTGCTCTATTTCCACGTGCACTATTCCACGATTGGGAACCTCCAGCAGCTAACAGAGCCACAATCAGGTCCTGATTCTGCTGAGATTTTGATTCTCAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.80% 44.60% 0.04% 0.51% NA
All Indica  2759 24.20% 75.00% 0.04% 0.80% NA
All Japonica  1512 99.50% 0.40% 0.07% 0.07% NA
Aus  269 93.70% 6.30% 0.00% 0.00% NA
Indica I  595 1.50% 97.80% 0.00% 0.67% NA
Indica II  465 38.70% 60.00% 0.00% 1.29% NA
Indica III  913 31.50% 67.90% 0.00% 0.55% NA
Indica Intermediate  786 24.30% 74.70% 0.13% 0.89% NA
Temperate Japonica  767 99.60% 0.30% 0.00% 0.13% NA
Tropical Japonica  504 99.20% 0.60% 0.20% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 77.80% 21.10% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0330783477 C -> T LOC_Os03g53690.1 upstream_gene_variant ; 4945.0bp to feature; MODIFIER silent_mutation Average:82.118; most accessible tissue: Callus, score: 91.332 N N N N
vg0330783477 C -> T LOC_Os03g53670.2 downstream_gene_variant ; 1645.0bp to feature; MODIFIER silent_mutation Average:82.118; most accessible tissue: Callus, score: 91.332 N N N N
vg0330783477 C -> T LOC_Os03g53680.1 downstream_gene_variant ; 4143.0bp to feature; MODIFIER silent_mutation Average:82.118; most accessible tissue: Callus, score: 91.332 N N N N
vg0330783477 C -> T LOC_Os03g53670.1 downstream_gene_variant ; 1645.0bp to feature; MODIFIER silent_mutation Average:82.118; most accessible tissue: Callus, score: 91.332 N N N N
vg0330783477 C -> T LOC_Os03g53670-LOC_Os03g53680 intergenic_region ; MODIFIER silent_mutation Average:82.118; most accessible tissue: Callus, score: 91.332 N N N N
vg0330783477 C -> DEL N N silent_mutation Average:82.118; most accessible tissue: Callus, score: 91.332 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)
vg0330783477 C T -0.02 0.01 0.01 0.0 0.02 0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0330783477 1.89E-07 1.10E-13 mr1050 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
vg0330783477 1.17E-06 1.94E-11 mr1050 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
vg0330783477 1.73E-07 2.14E-16 mr1272 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
vg0330783477 5.79E-07 1.42E-12 mr1272 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
vg0330783477 NA 9.41E-09 mr1354 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
vg0330783477 NA 3.47E-06 mr1595 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
vg0330783477 NA 3.98E-06 mr1607 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
vg0330783477 NA 1.72E-07 mr1699 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
vg0330783477 NA 8.36E-14 mr1726 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
vg0330783477 NA 1.88E-06 mr1789 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
vg0330783477 NA 1.79E-07 mr1829 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
vg0330783477 6.14E-08 2.67E-19 mr1829 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
vg0330783477 NA 6.56E-20 mr1842 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
vg0330783477 NA 8.99E-12 mr1842 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
vg0330783477 NA 7.06E-07 mr1850 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
vg0330783477 NA 4.10E-14 mr1902 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
vg0330783477 NA 1.87E-12 mr1902 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
vg0330783477 NA 6.50E-10 mr1935 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
vg0330783477 NA 6.48E-09 mr1036_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
vg0330783477 1.56E-07 1.43E-15 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
vg0330783477 1.90E-07 9.90E-13 mr1050_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
vg0330783477 NA 1.78E-09 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
vg0330783477 NA 1.44E-06 mr1272_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
vg0330783477 NA 1.24E-08 mr1354_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
vg0330783477 NA 8.36E-09 mr1699_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
vg0330783477 2.31E-07 5.30E-21 mr1829_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
vg0330783477 NA 6.42E-12 mr1842_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
vg0330783477 NA 1.15E-16 mr1902_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
vg0330783477 NA 7.17E-06 mr1923_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