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Detailed information for vg0613296114:

Variant ID: vg0613296114 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 13296114
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTAACAAACCATCTAAAAAAATATCTTCCTCCCTTCCATTCACCCCGCAACGGTTAAGGTTGTGATGGCAACGATATCGATAGGAGGTGACGAAGTGTGG[G/C]
GTAGCGTAGCAACGGGAGGCGGCAAAATGCGACGAGGTAGTGGTAGTAGGATGAAGTGGGGCTTCAATCCAATCCCCCTGCTCTCTCATTACTACCCCGC

Reverse complement sequence

GCGGGGTAGTAATGAGAGAGCAGGGGGATTGGATTGAAGCCCCACTTCATCCTACTACCACTACCTCGTCGCATTTTGCCGCCTCCCGTTGCTACGCTAC[C/G]
CCACACTTCGTCACCTCCTATCGATATCGTTGCCATCACAACCTTAACCGTTGCGGGGTGAATGGAAGGGAGGAAGATATTTTTTTAGATGGTTTGTTAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.50% 7.40% 0.13% 0.00% NA
All Indica  2759 98.90% 1.10% 0.00% 0.00% NA
All Japonica  1512 79.00% 20.70% 0.26% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 98.00% 2.00% 0.00% 0.00% NA
Temperate Japonica  767 97.30% 2.50% 0.26% 0.00% NA
Tropical Japonica  504 49.00% 50.80% 0.20% 0.00% NA
Japonica Intermediate  241 83.80% 15.80% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 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
vg0613296114 G -> C LOC_Os06g22810.1 upstream_gene_variant ; 973.0bp to feature; MODIFIER silent_mutation Average:77.051; most accessible tissue: Zhenshan97 panicle, score: 90.849 N N N N
vg0613296114 G -> C LOC_Os06g22800-LOC_Os06g22810 intergenic_region ; MODIFIER silent_mutation Average:77.051; most accessible tissue: Zhenshan97 panicle, score: 90.849 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)
vg0613296114 G C -0.07 -0.05 -0.02 -0.04 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0613296114 NA 2.00E-07 mr1229 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
vg0613296114 NA 3.29E-25 mr1301 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
vg0613296114 NA 7.69E-16 mr1410 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
vg0613296114 NA 8.22E-11 mr1993 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
vg0613296114 NA 3.71E-24 mr1301_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
vg0613296114 NA 7.36E-15 mr1410_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
vg0613296114 NA 7.15E-12 mr1993_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