Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0326817228:

Variant ID: vg0326817228 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 26817228
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.60, G: 0.40, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


CCCTAAACTACAAAACCAGATATCTGGCGTCCCTTAACTAATCAAAACCAGTCACAGCAGGTCCTTCGGTGGTTTTGGCCCCGATTTTGTCCTACGTGGC[A/G]
GCTGAGTCAGCGTGGGACCCACATGGACCCATGTCCCGGTGTCCACGTCACCACCCTCTCTCTTAATCTCTTTCCCCTCTTCTGCCCAGGACCGCCGCGC

Reverse complement sequence

GCGCGGCGGTCCTGGGCAGAAGAGGGGAAAGAGATTAAGAGAGAGGGTGGTGACGTGGACACCGGGACATGGGTCCATGTGGGTCCCACGCTGACTCAGC[T/C]
GCCACGTAGGACAAAATCGGGGCCAAAACCACCGAAGGACCTGCTGTGACTGGTTTTGATTAGTTAAGGGACGCCAGATATCTGGTTTTGTAGTTTAGGG

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 54.70% 45.30% 0.04% 0.00% NA
All Indica  2759 79.80% 20.10% 0.07% 0.00% NA
All Japonica  1512 1.30% 98.70% 0.00% 0.00% NA
Aus  269 95.90% 4.10% 0.00% 0.00% NA
Indica I  595 83.20% 16.60% 0.17% 0.00% NA
Indica II  465 96.30% 3.70% 0.00% 0.00% NA
Indica III  913 65.20% 34.80% 0.00% 0.00% NA
Indica Intermediate  786 84.60% 15.30% 0.13% 0.00% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 1.80% 98.20% 0.00% 0.00% NA
Japonica Intermediate  241 3.30% 96.70% 0.00% 0.00% NA
VI/Aromatic  96 57.30% 42.70% 0.00% 0.00% NA
Intermediate  90 52.20% 47.80% 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
vg0326817228 A -> G LOC_Os03g47430.1 upstream_gene_variant ; 4510.0bp to feature; MODIFIER silent_mutation Average:86.232; most accessible tissue: Zhenshan97 panicle, score: 94.112 N N N N
vg0326817228 A -> G LOC_Os03g47440.1 upstream_gene_variant ; 713.0bp to feature; MODIFIER silent_mutation Average:86.232; most accessible tissue: Zhenshan97 panicle, score: 94.112 N N N N
vg0326817228 A -> G LOC_Os03g47460.1 upstream_gene_variant ; 217.0bp to feature; MODIFIER silent_mutation Average:86.232; most accessible tissue: Zhenshan97 panicle, score: 94.112 N N N N
vg0326817228 A -> G LOC_Os03g47440-LOC_Os03g47460 intergenic_region ; MODIFIER silent_mutation Average:86.232; most accessible tissue: Zhenshan97 panicle, score: 94.112 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)
vg0326817228 A G -0.03 -0.03 -0.04 -0.04 -0.04 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0326817228 NA 4.41E-09 mr1722 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
vg0326817228 NA 1.02E-06 mr1063_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
vg0326817228 NA 7.85E-07 mr1180_2 Ind_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
vg0326817228 NA 2.18E-08 mr1322_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
vg0326817228 NA 6.89E-19 mr1336_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
vg0326817228 NA 5.82E-15 mr1579_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
vg0326817228 NA 5.97E-21 mr1627_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