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Detailed information for vg0503778745:

Variant ID: vg0503778745 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 3778745
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTCACTGCCACAAAACGGAATTGCCTGAAGCGCGTTCTATCTGCTGCTCCCCTTCTTCTGGGCTTCTGGCGAGATATTTAACTTTTTGCCATTTTTAG[G/A]
TGGCAATTAACTATTTGCCACTAGACCCACATGTCATAGAGATAGGGGTGGCAAATAGTGTTTCGTGCTCTTGCTTGCCGTTGATTACCCAACAGGCGGC

Reverse complement sequence

GCCGCCTGTTGGGTAATCAACGGCAAGCAAGAGCACGAAACACTATTTGCCACCCCTATCTCTATGACATGTGGGTCTAGTGGCAAATAGTTAATTGCCA[C/T]
CTAAAAATGGCAAAAAGTTAAATATCTCGCCAGAAGCCCAGAAGAAGGGGAGCAGCAGATAGAACGCGCTTCAGGCAATTCCGTTTTGTGGCAGTGAAGA

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 86.40% 8.10% 2.14% 3.36% NA
All Indica  2759 90.60% 0.70% 3.44% 5.29% NA
All Japonica  1512 76.30% 23.10% 0.20% 0.40% NA
Aus  269 97.80% 1.10% 0.74% 0.37% NA
Indica I  595 85.90% 0.00% 7.90% 6.22% NA
Indica II  465 78.30% 1.50% 5.38% 14.84% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 90.70% 1.30% 2.93% 5.09% NA
Temperate Japonica  767 94.90% 3.90% 0.39% 0.78% NA
Tropical Japonica  504 48.00% 52.00% 0.00% 0.00% NA
Japonica Intermediate  241 76.30% 23.70% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 77.80% 15.60% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0503778745 G -> DEL N N silent_mutation Average:80.08; most accessible tissue: Callus, score: 96.257 N N N N
vg0503778745 G -> A LOC_Os05g07140-LOC_Os05g07170 intergenic_region ; MODIFIER silent_mutation Average:80.08; most accessible tissue: Callus, score: 96.257 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)
vg0503778745 G A -0.08 -0.05 -0.02 -0.01 -0.05 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0503778745 NA 2.00E-06 mr1248 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
vg0503778745 NA 1.55E-06 mr1510 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
vg0503778745 NA 4.91E-06 mr1602 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
vg0503778745 NA 1.51E-06 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
vg0503778745 NA 2.25E-11 mr1800 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
vg0503778745 NA 1.40E-18 mr1301_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