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Detailed information for vg0328828618:

Variant ID: vg0328828618 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 28828618
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, T: 0.06, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


ATACTAAATTTTGGTTTTATATTGGTATTAAACCAAACATAGACTAGTTAACTTTGCCCTATCAAAAAATTGGTAGTGCCAAAATTTGACTAGATTTTAG[G/T]
ACTACCAATTAATTAGTAGGGTAGAAAGCCAAATAGGCCCATGGTGAGCTGGTGACTTATGTGCATACGTGTGAGAGCTGAGAAGCGATTCCACAGATCG

Reverse complement sequence

CGATCTGTGGAATCGCTTCTCAGCTCTCACACGTATGCACATAAGTCACCAGCTCACCATGGGCCTATTTGGCTTTCTACCCTACTAATTAATTGGTAGT[C/A]
CTAAAATCTAGTCAAATTTTGGCACTACCAATTTTTTGATAGGGCAAAGTTAACTAGTCTATGTTTGGTTTAATACCAATATAAAACCAAAATTTAGTAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 76.90% 22.90% 0.21% 0.00% NA
All Indica  2759 71.40% 28.30% 0.29% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 2.20% 97.40% 0.37% 0.00% NA
Indica I  595 95.00% 5.00% 0.00% 0.00% NA
Indica II  465 43.70% 55.70% 0.65% 0.00% NA
Indica III  913 70.40% 29.50% 0.11% 0.00% NA
Indica Intermediate  786 71.00% 28.50% 0.51% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 72.20% 26.70% 1.11% 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
vg0328828618 G -> T LOC_Os03g50490.1 upstream_gene_variant ; 2097.0bp to feature; MODIFIER silent_mutation Average:76.567; most accessible tissue: Minghui63 panicle, score: 96.661 N N N N
vg0328828618 G -> T LOC_Os03g50500.1 upstream_gene_variant ; 2208.0bp to feature; MODIFIER silent_mutation Average:76.567; most accessible tissue: Minghui63 panicle, score: 96.661 N N N N
vg0328828618 G -> T LOC_Os03g50490-LOC_Os03g50500 intergenic_region ; MODIFIER silent_mutation Average:76.567; most accessible tissue: Minghui63 panicle, score: 96.661 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)
vg0328828618 G T 0.04 0.01 0.0 0.0 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0328828618 NA 1.74E-07 mr1003 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
vg0328828618 4.55E-06 3.01E-06 mr1006 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
vg0328828618 NA 3.32E-07 mr1010 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
vg0328828618 NA 1.54E-07 mr1051 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
vg0328828618 3.64E-06 3.24E-06 mr1052 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
vg0328828618 NA 9.01E-07 mr1163 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
vg0328828618 NA 5.51E-06 mr1192 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
vg0328828618 NA 3.99E-11 mr1193 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
vg0328828618 NA 2.49E-06 mr1193 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
vg0328828618 NA 7.07E-06 mr1536 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
vg0328828618 NA 1.34E-07 mr1587 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
vg0328828618 NA 7.50E-06 mr1668 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
vg0328828618 NA 4.15E-07 mr1931 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
vg0328828618 NA 1.73E-13 mr1193_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
vg0328828618 NA 1.61E-07 mr1952_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