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Detailed information for vg0626092258:

Variant ID: vg0626092258 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 26092258
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


ACGATAAACCTTACCCTATTTAATTTTCCCTACTGAATTTTATCCTTATTAATTTAATTTAACAAAGTCAACTTGATTTCCTCAATGGGCATTTTTATGT[C/G]
GCATATATGCTTGCGTGCGCGCTTCATGCATGTCAATAACTTAGTATACCATACTAATCTATGTAATGAACCCAATCGTCTTGGAACAGCTCTCGCCATG

Reverse complement sequence

CATGGCGAGAGCTGTTCCAAGACGATTGGGTTCATTACATAGATTAGTATGGTATACTAAGTTATTGACATGCATGAAGCGCGCACGCAAGCATATATGC[G/C]
ACATAAAAATGCCCATTGAGGAAATCAAGTTGACTTTGTTAAATTAAATTAATAAGGATAAAATTCAGTAGGGAAAATTAAATAGGGTAAGGTTTATCGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.90% 35.00% 0.11% 0.00% NA
All Indica  2759 46.20% 53.60% 0.11% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 53.50% 46.10% 0.37% 0.00% NA
Indica I  595 22.20% 77.80% 0.00% 0.00% NA
Indica II  465 26.70% 73.10% 0.22% 0.00% NA
Indica III  913 65.00% 34.90% 0.11% 0.00% NA
Indica Intermediate  786 54.30% 45.50% 0.13% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 80.20% 19.80% 0.00% 0.00% NA
Intermediate  90 71.10% 27.80% 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
vg0626092258 C -> G LOC_Os06g43410.1 upstream_gene_variant ; 258.0bp to feature; MODIFIER silent_mutation Average:72.782; most accessible tissue: Callus, score: 98.327 N N N N
vg0626092258 C -> G LOC_Os06g43420.1 downstream_gene_variant ; 4896.0bp to feature; MODIFIER silent_mutation Average:72.782; most accessible tissue: Callus, score: 98.327 N N N N
vg0626092258 C -> G LOC_Os06g43384-LOC_Os06g43410 intergenic_region ; MODIFIER silent_mutation Average:72.782; most accessible tissue: Callus, score: 98.327 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)
vg0626092258 C G -0.03 0.05 0.02 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0626092258 3.75E-06 NA mr1327 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
vg0626092258 NA 4.08E-09 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
vg0626092258 NA 2.97E-08 mr1349_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
vg0626092258 1.44E-06 7.60E-08 mr1355_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
vg0626092258 NA 1.75E-06 mr1452_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
vg0626092258 5.59E-06 3.03E-07 mr1462_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
vg0626092258 2.81E-06 1.75E-07 mr1470_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
vg0626092258 NA 4.89E-06 mr1472_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
vg0626092258 NA 3.03E-07 mr1623_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
vg0626092258 NA 9.33E-07 mr1719_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
vg0626092258 1.07E-07 3.49E-08 mr1761_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
vg0626092258 5.43E-06 7.69E-09 mr1899_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