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Detailed information for vg0203254325:

Variant ID: vg0203254325 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 3254325
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: 119. )

Flanking Sequence (100 bp) in Reference Genome:


AGAACATTTTTACATATAAGCTGTGTTTAGATCTAAAGTTTGGATCTAAATTTCAGTCATTTTCCATCACATCAACCTATCATATACACACAACTTTTCA[G/A]
TCATATCATCTCCAATTTCAAACAAAATTTAAACTTTGCGCTGAACTAAACACAAAACACAGCCATAGAAACATGAACCGCGCACACACATGTGCCGTGC

Reverse complement sequence

GCACGGCACATGTGTGTGCGCGGTTCATGTTTCTATGGCTGTGTTTTGTGTTTAGTTCAGCGCAAAGTTTAAATTTTGTTTGAAATTGGAGATGATATGA[C/T]
TGAAAAGTTGTGTGTATATGATAGGTTGATGTGATGGAAAATGACTGAAATTTAGATCCAAACTTTAGATCTAAACACAGCTTATATGTAAAAATGTTCT

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 75.60% 21.10% 3.26% 0.00% NA
All Indica  2759 70.30% 26.50% 3.15% 0.00% NA
All Japonica  1512 79.60% 16.30% 4.10% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 52.10% 38.00% 9.92% 0.00% NA
Indica II  465 56.30% 41.90% 1.72% 0.00% NA
Indica III  913 88.80% 11.10% 0.11% 0.00% NA
Indica Intermediate  786 70.90% 26.70% 2.42% 0.00% NA
Temperate Japonica  767 72.90% 21.00% 6.13% 0.00% NA
Tropical Japonica  504 96.60% 2.40% 0.99% 0.00% NA
Japonica Intermediate  241 65.60% 30.30% 4.15% 0.00% NA
VI/Aromatic  96 91.70% 6.20% 2.08% 0.00% NA
Intermediate  90 85.60% 11.10% 3.33% 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
vg0203254325 G -> A LOC_Os02g06500.1 upstream_gene_variant ; 4593.0bp to feature; MODIFIER silent_mutation Average:89.24; most accessible tissue: Zhenshan97 flag leaf, score: 93.97 N N N N
vg0203254325 G -> A LOC_Os02g06520.1 upstream_gene_variant ; 600.0bp to feature; MODIFIER silent_mutation Average:89.24; most accessible tissue: Zhenshan97 flag leaf, score: 93.97 N N N N
vg0203254325 G -> A LOC_Os02g06510.1 downstream_gene_variant ; 1930.0bp to feature; MODIFIER silent_mutation Average:89.24; most accessible tissue: Zhenshan97 flag leaf, score: 93.97 N N N N
vg0203254325 G -> A LOC_Os02g06510-LOC_Os02g06520 intergenic_region ; MODIFIER silent_mutation Average:89.24; most accessible tissue: Zhenshan97 flag leaf, score: 93.97 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)
vg0203254325 G A -0.01 -0.01 -0.01 -0.03 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0203254325 1.22E-07 1.22E-07 mr1008 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
vg0203254325 1.37E-07 1.37E-07 mr1009 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
vg0203254325 1.33E-07 1.33E-07 mr1014 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
vg0203254325 3.04E-06 3.04E-06 mr1015 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
vg0203254325 NA 2.66E-06 mr1118 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
vg0203254325 NA 1.82E-06 mr1197 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
vg0203254325 NA 9.63E-06 mr1582_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