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Detailed information for vg1208182733:

Variant ID: vg1208182733 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 8182733
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, C: 0.04, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


TAATTTGTGCCTGCCCATATCCATGTGCCAATGAGCGTCCTGTTTGATGTACGGTTGGTCTGGCTAGACATCGCTCACTGTGCTCTGGAAACATCGTAGG[T/C]
GCCTGTGACCTGCCTATGATTTCGTTCTTCCATCTCACACGCAATCCCGCGTCTCCATTCATTCATCTTTCGATCGCGCCTCTACACCTGACCTTTTACG

Reverse complement sequence

CGTAAAAGGTCAGGTGTAGAGGCGCGATCGAAAGATGAATGAATGGAGACGCGGGATTGCGTGTGAGATGGAAGAACGAAATCATAGGCAGGTCACAGGC[A/G]
CCTACGATGTTTCCAGAGCACAGTGAGCGATGTCTAGCCAGACCAACCGTACATCAAACAGGACGCTCATTGGCACATGGATATGGGCAGGCACAAATTA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 48.30% 26.90% 0.83% 23.91% NA
All Indica  2759 49.70% 37.60% 0.62% 12.11% NA
All Japonica  1512 52.40% 4.60% 0.86% 42.13% NA
Aus  269 20.10% 30.50% 1.86% 47.58% NA
Indica I  595 37.30% 46.20% 0.34% 16.13% NA
Indica II  465 41.10% 51.00% 0.86% 7.10% NA
Indica III  913 60.50% 27.50% 0.66% 11.39% NA
Indica Intermediate  786 51.50% 35.00% 0.64% 12.85% NA
Temperate Japonica  767 75.40% 6.30% 0.52% 17.86% NA
Tropical Japonica  504 24.00% 2.60% 1.39% 72.02% NA
Japonica Intermediate  241 38.60% 3.70% 0.83% 56.85% NA
VI/Aromatic  96 20.80% 66.70% 1.04% 11.46% NA
Intermediate  90 54.40% 20.00% 3.33% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1208182733 T -> C LOC_Os12g14360.1 upstream_gene_variant ; 855.0bp to feature; MODIFIER silent_mutation Average:66.272; most accessible tissue: Minghui63 panicle, score: 85.069 N N N N
vg1208182733 T -> C LOC_Os12g14360-LOC_Os12g14374 intergenic_region ; MODIFIER silent_mutation Average:66.272; most accessible tissue: Minghui63 panicle, score: 85.069 N N N N
vg1208182733 T -> DEL N N silent_mutation Average:66.272; most accessible tissue: Minghui63 panicle, score: 85.069 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)
vg1208182733 T C 0.0 0.01 0.02 -0.03 -0.05 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1208182733 NA 1.41E-08 mr1049 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
vg1208182733 NA 2.25E-11 mr1138 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
vg1208182733 NA 3.63E-07 mr1425 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
vg1208182733 NA 4.82E-09 mr1425 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
vg1208182733 NA 7.00E-06 mr1558 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
vg1208182733 NA 1.55E-07 mr1577 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
vg1208182733 NA 6.69E-06 mr1826 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
vg1208182733 NA 1.44E-06 mr1002_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
vg1208182733 NA 2.46E-09 mr1864_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