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Detailed information for vg1204217058:

Variant ID: vg1204217058 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 4217058
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.10, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


CAAATCGTTTCCTGATGCATCTGTCACCAGACCTCCAGCTTCTGAAAACAGCACAAGCAGAATATCAATCTAAAATGTTTCAGTTGGTTTCTACGTTTTA[G/A]
CACAAGCAGAATATCAATCTAAAATGTTTCAGTTGGGTTCTATGTTTTTTTTCAGGTTGTTGGGTTCTATGTTTTCAATGTTCAAAAAGAGAACCTTCAT

Reverse complement sequence

ATGAAGGTTCTCTTTTTGAACATTGAAAACATAGAACCCAACAACCTGAAAAAAAACATAGAACCCAACTGAAACATTTTAGATTGATATTCTGCTTGTG[C/T]
TAAAACGTAGAAACCAACTGAAACATTTTAGATTGATATTCTGCTTGTGCTGTTTTCAGAAGCTGGAGGTCTGGTGACAGATGCATCAGGAAACGATTTG

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 78.80% 21.10% 0.08% 0.00% NA
All Indica  2759 87.40% 12.40% 0.14% 0.00% NA
All Japonica  1512 70.40% 29.60% 0.00% 0.00% NA
Aus  269 62.50% 37.50% 0.00% 0.00% NA
Indica I  595 92.10% 7.90% 0.00% 0.00% NA
Indica II  465 80.40% 19.60% 0.00% 0.00% NA
Indica III  913 88.90% 11.10% 0.00% 0.00% NA
Indica Intermediate  786 86.30% 13.20% 0.51% 0.00% NA
Temperate Japonica  767 86.00% 14.00% 0.00% 0.00% NA
Tropical Japonica  504 55.40% 44.60% 0.00% 0.00% NA
Japonica Intermediate  241 52.30% 47.70% 0.00% 0.00% NA
VI/Aromatic  96 12.50% 87.50% 0.00% 0.00% NA
Intermediate  90 74.40% 25.60% 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
vg1204217058 G -> A LOC_Os12g08270.1 upstream_gene_variant ; 705.0bp to feature; MODIFIER silent_mutation Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659 N N N N
vg1204217058 G -> A LOC_Os12g08260.1 downstream_gene_variant ; 3583.0bp to feature; MODIFIER silent_mutation Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659 N N N N
vg1204217058 G -> A LOC_Os12g08290.1 downstream_gene_variant ; 3620.0bp to feature; MODIFIER silent_mutation Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659 N N N N
vg1204217058 G -> A LOC_Os12g08260.4 downstream_gene_variant ; 3583.0bp to feature; MODIFIER silent_mutation Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659 N N N N
vg1204217058 G -> A LOC_Os12g08260.6 downstream_gene_variant ; 3583.0bp to feature; MODIFIER silent_mutation Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659 N N N N
vg1204217058 G -> A LOC_Os12g08260.7 downstream_gene_variant ; 3583.0bp to feature; MODIFIER silent_mutation Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659 N N N N
vg1204217058 G -> A LOC_Os12g08260.2 downstream_gene_variant ; 3583.0bp to feature; MODIFIER silent_mutation Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659 N N N N
vg1204217058 G -> A LOC_Os12g08260.5 downstream_gene_variant ; 3583.0bp to feature; MODIFIER silent_mutation Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659 N N N N
vg1204217058 G -> A LOC_Os12g08260.3 downstream_gene_variant ; 3583.0bp to feature; MODIFIER silent_mutation Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659 N N N N
vg1204217058 G -> A LOC_Os12g08280.1 intron_variant ; MODIFIER silent_mutation Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659 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)
vg1204217058 G A 0.01 0.0 -0.01 -0.01 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1204217058 NA 2.18E-06 mr1180 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
vg1204217058 NA 1.87E-08 mr1180_2 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
vg1204217058 NA 1.87E-07 mr1183_2 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