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Detailed information for vg0229221640:

Variant ID: vg0229221640 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 29221640
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


CCATATGTCGTCTAATAATCATCTTCGTCTCTTAACAATTTGGAAAGCGCCTTTTGTCGAAAAGACACCCTTGAAAAACCATTAGGATCATCACAGCCCA[G/C]
TCTCATGTTGCATACATAGCCTGAGTGTCTCGCACCCTCACCAACCAACAACCTACTAGCCAGTACATCCTAAGTTTCTTCATCACATTACTAGTACAAG

Reverse complement sequence

CTTGTACTAGTAATGTGATGAAGAAACTTAGGATGTACTGGCTAGTAGGTTGTTGGTTGGTGAGGGTGCGAGACACTCAGGCTATGTATGCAACATGAGA[C/G]
TGGGCTGTGATGATCCTAATGGTTTTTCAAGGGTGTCTTTTCGACAAAAGGCGCTTTCCAAATTGTTAAGAGACGAAGATGATTATTAGACGACATATGG

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 70.80% 28.30% 0.91% 0.00% NA
All Indica  2759 98.00% 2.00% 0.07% 0.00% NA
All Japonica  1512 21.90% 75.80% 2.31% 0.00% NA
Aus  269 89.20% 9.30% 1.49% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 97.00% 2.80% 0.22% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 95.50% 4.30% 0.13% 0.00% NA
Temperate Japonica  767 5.20% 92.80% 1.96% 0.00% NA
Tropical Japonica  504 39.90% 58.10% 1.98% 0.00% NA
Japonica Intermediate  241 37.30% 58.50% 4.15% 0.00% NA
VI/Aromatic  96 24.00% 74.00% 2.08% 0.00% NA
Intermediate  90 52.20% 47.80% 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
vg0229221640 G -> C LOC_Os02g47780.1 downstream_gene_variant ; 2233.0bp to feature; MODIFIER silent_mutation Average:66.325; most accessible tissue: Zhenshan97 flower, score: 91.937 N N N N
vg0229221640 G -> C LOC_Os02g47790.1 downstream_gene_variant ; 4988.0bp to feature; MODIFIER silent_mutation Average:66.325; most accessible tissue: Zhenshan97 flower, score: 91.937 N N N N
vg0229221640 G -> C LOC_Os02g47770-LOC_Os02g47780 intergenic_region ; MODIFIER silent_mutation Average:66.325; most accessible tissue: Zhenshan97 flower, score: 91.937 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)
vg0229221640 G C -0.01 0.0 -0.02 -0.03 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0229221640 6.83E-06 8.36E-07 mr1136 Jap_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
vg0229221640 NA 2.72E-06 mr1906 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
vg0229221640 NA 1.61E-13 mr1496_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