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Detailed information for vg0123550945:

Variant ID: vg0123550945 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 23550945
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


ACCCCGACGTGGCCAGAAGGCCATGCCAAGGGCCGCTTTCCTTCCTTCTACCATGCCTTCTCCTCTGCTCTGCTCTTGGCCCGCTGAAGCTGCCGATGGC[C/T]
GTCCCCCCTAGTCGAGCTAGTCAGTGTCATCGCTGTATGCCTATGAGGGAAAGAAGAGGGAACAAAGAGAAGAGGAGGAGAGGAGAAGAAATATGTGACA

Reverse complement sequence

TGTCACATATTTCTTCTCCTCTCCTCCTCTTCTCTTTGTTCCCTCTTCTTTCCCTCATAGGCATACAGCGATGACACTGACTAGCTCGACTAGGGGGGAC[G/A]
GCCATCGGCAGCTTCAGCGGGCCAAGAGCAGAGCAGAGGAGAAGGCATGGTAGAAGGAAGGAAAGCGGCCCTTGGCATGGCCTTCTGGCCACGTCGGGGT

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 79.30% 20.50% 0.00% 0.23% NA
All Indica  2759 65.90% 33.70% 0.00% 0.36% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 95.50% 4.50% 0.00% 0.00% NA
Indica I  595 96.30% 3.70% 0.00% 0.00% NA
Indica II  465 63.90% 35.30% 0.00% 0.86% NA
Indica III  913 49.10% 50.80% 0.00% 0.11% NA
Indica Intermediate  786 63.60% 35.80% 0.00% 0.64% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.40% 1.60% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 15.60% 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
vg0123550945 C -> T LOC_Os01g41580.1 upstream_gene_variant ; 4008.0bp to feature; MODIFIER silent_mutation Average:90.487; most accessible tissue: Callus, score: 99.468 N N N N
vg0123550945 C -> T LOC_Os01g41590.1 upstream_gene_variant ; 1851.0bp to feature; MODIFIER silent_mutation Average:90.487; most accessible tissue: Callus, score: 99.468 N N N N
vg0123550945 C -> T LOC_Os01g41600.1 upstream_gene_variant ; 1025.0bp to feature; MODIFIER silent_mutation Average:90.487; most accessible tissue: Callus, score: 99.468 N N N N
vg0123550945 C -> T LOC_Os01g41610.1 downstream_gene_variant ; 2738.0bp to feature; MODIFIER silent_mutation Average:90.487; most accessible tissue: Callus, score: 99.468 N N N N
vg0123550945 C -> T LOC_Os01g41610.2 downstream_gene_variant ; 3309.0bp to feature; MODIFIER silent_mutation Average:90.487; most accessible tissue: Callus, score: 99.468 N N N N
vg0123550945 C -> T LOC_Os01g41590-LOC_Os01g41600 intergenic_region ; MODIFIER silent_mutation Average:90.487; most accessible tissue: Callus, score: 99.468 N N N N
vg0123550945 C -> DEL N N silent_mutation Average:90.487; most accessible tissue: Callus, score: 99.468 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)
vg0123550945 C T 0.02 0.01 0.01 0.03 0.03 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0123550945 NA 1.52E-08 mr1380 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
vg0123550945 NA 6.76E-06 mr1380 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
vg0123550945 NA 2.91E-12 mr1561 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
vg0123550945 NA 2.41E-08 mr1561 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
vg0123550945 NA 1.86E-06 mr1807 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
vg0123550945 NA 3.60E-09 mr1875 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
vg0123550945 4.97E-06 6.92E-11 mr1908 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
vg0123550945 NA 1.10E-06 mr1908 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
vg0123550945 NA 2.44E-06 mr1936 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
vg0123550945 NA 2.01E-06 mr1937 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
vg0123550945 8.36E-07 8.36E-07 mr1996 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
vg0123550945 NA 2.83E-11 mr1380_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
vg0123550945 NA 3.76E-08 mr1380_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
vg0123550945 NA 2.76E-13 mr1561_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
vg0123550945 NA 6.77E-09 mr1561_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
vg0123550945 NA 2.40E-11 mr1875_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
vg0123550945 NA 2.01E-06 mr1875_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
vg0123550945 NA 7.35E-13 mr1908_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
vg0123550945 NA 1.51E-07 mr1908_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
vg0123550945 NA 3.60E-10 mr1996_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
vg0123550945 NA 4.56E-07 mr1996_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