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Detailed information for vg0623452196:

Variant ID: vg0623452196 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 23452196
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTGCAACATGCCGGCGATGTGCGACCCTGGCAACGGGGAAGCCTACCGCGGCGTGGCCAGTGCCAACGACTAAACGACACGCCATGGCGCGCCGGCGGTG[G/A]
CAGCGAAGGAGCTGCTCAAGTGCTCAGCGCCATGGTTGTGCCCGCCATTGCTAACTCACACCGCAGATGAAATCAACACAACCTAACTTAGCTAGATCAC

Reverse complement sequence

GTGATCTAGCTAAGTTAGGTTGTGTTGATTTCATCTGCGGTGTGAGTTAGCAATGGCGGGCACAACCATGGCGCTGAGCACTTGAGCAGCTCCTTCGCTG[C/T]
CACCGCCGGCGCGCCATGGCGTGTCGTTTAGTCGTTGGCACTGGCCACGCCGCGGTAGGCTTCCCCGTTGCCAGGGTCGCACATCGCCGGCATGTTGCAC

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 94.80% 5.20% 0.00% 0.00% NA
All Indica  2759 97.80% 2.20% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 34.20% 65.80% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 96.80% 3.20% 0.00% 0.00% NA
Indica Intermediate  786 97.20% 2.80% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0623452196 G -> A LOC_Os06g39480.1 upstream_gene_variant ; 2743.0bp to feature; MODIFIER silent_mutation Average:94.232; most accessible tissue: Zhenshan97 flower, score: 97.674 N N N N
vg0623452196 G -> A LOC_Os06g39500.1 upstream_gene_variant ; 16.0bp to feature; MODIFIER silent_mutation Average:94.232; most accessible tissue: Zhenshan97 flower, score: 97.674 N N N N
vg0623452196 G -> A LOC_Os06g39510.1 upstream_gene_variant ; 4390.0bp to feature; MODIFIER silent_mutation Average:94.232; most accessible tissue: Zhenshan97 flower, score: 97.674 N N N N
vg0623452196 G -> A LOC_Os06g39500-LOC_Os06g39510 intergenic_region ; MODIFIER silent_mutation Average:94.232; most accessible tissue: Zhenshan97 flower, score: 97.674 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)
vg0623452196 G A 0.17 0.18 0.1 0.0 0.06 0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0623452196 NA 9.32E-07 mr1006 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
vg0623452196 NA 1.44E-06 mr1052 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
vg0623452196 NA 5.70E-07 mr1060 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
vg0623452196 NA 4.30E-07 mr1073 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
vg0623452196 NA 3.26E-06 mr1126 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
vg0623452196 NA 1.42E-06 mr1230 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
vg0623452196 NA 3.36E-10 mr1232 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
vg0623452196 NA 8.73E-06 mr1331 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
vg0623452196 NA 9.85E-06 mr1424 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
vg0623452196 NA 4.69E-06 mr1523 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
vg0623452196 NA 7.76E-42 mr1550 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
vg0623452196 NA 2.44E-09 mr1621 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
vg0623452196 NA 9.97E-06 mr1634 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
vg0623452196 NA 7.44E-08 mr1669 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
vg0623452196 NA 1.52E-07 mr1931 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
vg0623452196 NA 6.32E-31 mr1549_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
vg0623452196 NA 1.11E-42 mr1550_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