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Detailed information for vg0602120650:

Variant ID: vg0602120650 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 2120650
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


AAAATAAAACAAATAATTAAACTTATGTTAAAAAAATCAATAACATCATGCATTAAAATACAAATGGTGTACGTAATGAGTAAGCTTGCACGTACTCCTG[T/C]
AATATAATGCCGACTGGCGGACAGCTAGTTGCAGTGTTAAGGAGTACTTACTTAGGTTTTAAACCATAATTTAATCTCCAATTACAGGAGGGATTAACTT

Reverse complement sequence

AAGTTAATCCCTCCTGTAATTGGAGATTAAATTATGGTTTAAAACCTAAGTAAGTACTCCTTAACACTGCAACTAGCTGTCCGCCAGTCGGCATTATATT[A/G]
CAGGAGTACGTGCAAGCTTACTCATTACGTACACCATTTGTATTTTAATGCATGATGTTATTGATTTTTTTAACATAAGTTTAATTATTTGTTTTATTTT

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 92.60% 7.30% 0.13% 0.00% NA
All Indica  2759 99.20% 0.80% 0.00% 0.00% NA
All Japonica  1512 82.10% 17.50% 0.40% 0.00% NA
Aus  269 79.90% 20.10% 0.00% 0.00% NA
Indica I  595 97.60% 2.40% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 0.00% 0.00% NA
Temperate Japonica  767 69.20% 30.00% 0.78% 0.00% NA
Tropical Japonica  504 96.80% 3.20% 0.00% 0.00% NA
Japonica Intermediate  241 92.50% 7.50% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0602120650 T -> C LOC_Os06g04840.1 upstream_gene_variant ; 4086.0bp to feature; MODIFIER silent_mutation Average:75.203; most accessible tissue: Zhenshan97 flower, score: 94.616 N N N N
vg0602120650 T -> C LOC_Os06g04850.1 upstream_gene_variant ; 2748.0bp to feature; MODIFIER silent_mutation Average:75.203; most accessible tissue: Zhenshan97 flower, score: 94.616 N N N N
vg0602120650 T -> C LOC_Os06g04840.2 upstream_gene_variant ; 4086.0bp to feature; MODIFIER silent_mutation Average:75.203; most accessible tissue: Zhenshan97 flower, score: 94.616 N N N N
vg0602120650 T -> C LOC_Os06g04840-LOC_Os06g04850 intergenic_region ; MODIFIER silent_mutation Average:75.203; most accessible tissue: Zhenshan97 flower, score: 94.616 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)
vg0602120650 T C -0.02 0.01 0.0 0.02 0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0602120650 NA 2.22E-06 mr1030 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
vg0602120650 NA 5.00E-06 mr1280 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
vg0602120650 2.26E-06 1.43E-06 mr1545 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
vg0602120650 NA 8.57E-06 mr1614 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
vg0602120650 NA 8.16E-07 mr1741 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
vg0602120650 NA 2.79E-06 mr1748 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
vg0602120650 NA 4.17E-06 mr1757_2 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