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Detailed information for vg0500963531:

Variant ID: vg0500963531 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 963531
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

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

Flanking Sequence (100 bp) in Reference Genome:


GAACTTTCCTAAACACACAAATTTCCAACTTTTAGGTTACATAATTCCAATTTCTTCAAACTTTTAATTTTGACGTGGAACTAAACATAGCCTTAGTACT[A/G]
CTGCTTCCCATGCTTGCTGTTTTCTTTTAGAAACTTTGATGCAAGATCTCAGTCCAGCACGAAGAAGTAGCTAGAGAGGCCACTTCTGAAAAGAGCAACT

Reverse complement sequence

AGTTGCTCTTTTCAGAAGTGGCCTCTCTAGCTACTTCTTCGTGCTGGACTGAGATCTTGCATCAAAGTTTCTAAAAGAAAACAGCAAGCATGGGAAGCAG[T/C]
AGTACTAAGGCTATGTTTAGTTCCACGTCAAAATTAAAAGTTTGAAGAAATTGGAATTATGTAACCTAAAAGTTGGAAATTTGTGTGTTTAGGAAAGTTC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.00% 4.70% 0.23% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 85.30% 14.00% 0.73% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 91.30% 8.00% 0.78% 0.00% NA
Tropical Japonica  504 79.00% 20.60% 0.40% 0.00% NA
Japonica Intermediate  241 79.70% 19.10% 1.24% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0500963531 A -> G LOC_Os05g02700.1 upstream_gene_variant ; 3590.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500963531 A -> G LOC_Os05g02700-LOC_Os05g02710 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 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)
vg0500963531 A G 0.0 0.0 0.0 -0.01 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0500963531 1.53E-06 1.53E-06 mr1160 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
vg0500963531 7.37E-06 NA mr1194 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
vg0500963531 NA 6.03E-08 mr1194 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
vg0500963531 NA 4.80E-07 mr1668 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