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Detailed information for vg0224416114:

Variant ID: vg0224416114 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24416114
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, G: 0.07, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


CGAATTCTTTTTTATGATAAAATTGCCACGCAAGCAACACGTTAGCATGAGTGGACCAAATTAACGTGCCAAACCGCTATCCCGGACTGCCAAAGTACTA[T/G]
ATTTGCATTGGTTTTGTGAGTTGAATTGCACCGCAGTTGAGAGGCGCAAATTGAATTCGACTTATACTTAAGGGATATTAGTGGACTTTATTCTTTTTGT

Reverse complement sequence

ACAAAAAGAATAAAGTCCACTAATATCCCTTAAGTATAAGTCGAATTCAATTTGCGCCTCTCAACTGCGGTGCAATTCAACTCACAAAACCAATGCAAAT[A/C]
TAGTACTTTGGCAGTCCGGGATAGCGGTTTGGCACGTTAATTTGGTCCACTCATGCTAACGTGTTGCTTGCGTGGCAATTTTATCATAAAAAAGAATTCG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.60% 7.90% 0.11% 21.35% NA
All Indica  2759 76.40% 8.70% 0.07% 14.86% NA
All Japonica  1512 59.20% 6.30% 0.20% 34.26% NA
Aus  269 75.50% 7.80% 0.00% 16.73% NA
Indica I  595 73.60% 2.00% 0.17% 24.20% NA
Indica II  465 85.80% 10.10% 0.00% 4.09% NA
Indica III  913 68.80% 11.90% 0.00% 19.28% NA
Indica Intermediate  786 81.70% 9.20% 0.13% 9.03% NA
Temperate Japonica  767 51.00% 5.90% 0.13% 43.02% NA
Tropical Japonica  504 73.80% 9.10% 0.20% 16.87% NA
Japonica Intermediate  241 54.80% 2.10% 0.41% 42.74% NA
VI/Aromatic  96 74.00% 6.20% 0.00% 19.79% NA
Intermediate  90 67.80% 13.30% 0.00% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0224416114 T -> G LOC_Os02g40330.1 upstream_gene_variant ; 2030.0bp to feature; MODIFIER silent_mutation Average:94.995; most accessible tissue: Zhenshan97 root, score: 99.039 N N N N
vg0224416114 T -> G LOC_Os02g40330.2 upstream_gene_variant ; 2030.0bp to feature; MODIFIER silent_mutation Average:94.995; most accessible tissue: Zhenshan97 root, score: 99.039 N N N N
vg0224416114 T -> G LOC_Os02g40330.3 upstream_gene_variant ; 2030.0bp to feature; MODIFIER silent_mutation Average:94.995; most accessible tissue: Zhenshan97 root, score: 99.039 N N N N
vg0224416114 T -> G LOC_Os02g40330-LOC_Os02g40340 intergenic_region ; MODIFIER silent_mutation Average:94.995; most accessible tissue: Zhenshan97 root, score: 99.039 N N N N
vg0224416114 T -> DEL N N silent_mutation Average:94.995; most accessible tissue: Zhenshan97 root, score: 99.039 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)
vg0224416114 T G -0.03 0.01 0.0 -0.01 -0.02 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224416114 7.20E-07 NA mr1013_2 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