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Detailed information for vg0123800969:

Variant ID: vg0123800969 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 23800969
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.05, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


CGGCGATCATCGCCGCCGCCACGGCCGGCGAACGACGCTCCAGCCGGCGGAGGTGACCCAACCCAGCCACCGCCGGCGAAATCCCGGAAGACGTCACACC[A/G]
CACCGCCATCGACTCCCTCGGCGAGGACCTCCTGCTGGACATCTTCCTCCGCCTCCCCACCCTCGCCTCGCTCGTCCGCGCCGCGCTCACCTGCCGGGCG

Reverse complement sequence

CGCCCGGCAGGTGAGCGCGGCGCGGACGAGCGAGGCGAGGGTGGGGAGGCGGAGGAAGATGTCCAGCAGGAGGTCCTCGCCGAGGGAGTCGATGGCGGTG[T/C]
GGTGTGACGTCTTCCGGGATTTCGCCGGCGGTGGCTGGGTTGGGTCACCTCCGCCGGCTGGAGCGTCGTTCGCCGGCCGTGGCGGCGGCGATGATCGCCG

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 78.10% 21.90% 0.04% 0.00% NA
All Indica  2759 97.80% 2.10% 0.07% 0.00% NA
All Japonica  1512 38.00% 62.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 97.50% 2.50% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 96.20% 3.60% 0.25% 0.00% NA
Temperate Japonica  767 22.80% 77.20% 0.00% 0.00% NA
Tropical Japonica  504 59.70% 40.30% 0.00% 0.00% NA
Japonica Intermediate  241 41.10% 58.90% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 66.70% 33.30% 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
vg0123800969 A -> G LOC_Os01g41970.1 upstream_gene_variant ; 305.0bp to feature; MODIFIER silent_mutation Average:90.156; most accessible tissue: Zhenshan97 flower, score: 94.812 N N N N
vg0123800969 A -> G LOC_Os01g41960.1 downstream_gene_variant ; 3997.0bp to feature; MODIFIER silent_mutation Average:90.156; most accessible tissue: Zhenshan97 flower, score: 94.812 N N N N
vg0123800969 A -> G LOC_Os01g41960-LOC_Os01g41970 intergenic_region ; MODIFIER silent_mutation Average:90.156; most accessible tissue: Zhenshan97 flower, score: 94.812 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)
vg0123800969 A G 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
vg0123800969 8.23E-07 NA mr1071 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
vg0123800969 1.55E-07 NA mr1080 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
vg0123800969 1.59E-06 NA mr1140 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
vg0123800969 2.12E-06 NA mr1203 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
vg0123800969 NA 8.26E-16 mr1484 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
vg0123800969 2.04E-06 NA mr1618 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
vg0123800969 NA 9.42E-07 mr1815 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
vg0123800969 NA 4.92E-07 mr1837 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
vg0123800969 NA 7.53E-06 mr1925 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