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Detailed information for vg0224673406:

Variant ID: vg0224673406 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24673406
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.62, C: 0.39, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


AGATTTGGAATCCAGATACTAAGGCCGTGTTTAGTTTTCCCCCTATTATCAACTTTCCATCATATTATATTACATCAAAAAATTTTCTACACATAAACTT[T/C]
CAACTTTTTTTTTCTGAACTCCCAACTTTCTTCGAACTTCCAATTTTTTTCAGGAACTAAACACACCCTAATGTAGCATTGCATTAGCATGTTGACAAAA

Reverse complement sequence

TTTTGTCAACATGCTAATGCAATGCTACATTAGGGTGTGTTTAGTTCCTGAAAAAAATTGGAAGTTCGAAGAAAGTTGGGAGTTCAGAAAAAAAAAGTTG[A/G]
AAGTTTATGTGTAGAAAATTTTTTGATGTAATATAATATGATGGAAAGTTGATAATAGGGGGAAAACTAAACACGGCCTTAGTATCTGGATTCCAAATCT

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 85.80% 12.60% 1.02% 0.61% NA
All Indica  2759 92.10% 5.80% 1.20% 0.91% NA
All Japonica  1512 73.90% 25.90% 0.26% 0.00% NA
Aus  269 90.30% 4.80% 3.72% 1.12% NA
Indica I  595 98.80% 1.20% 0.00% 0.00% NA
Indica II  465 89.00% 4.70% 3.44% 2.80% NA
Indica III  913 91.00% 7.80% 0.99% 0.22% NA
Indica Intermediate  786 90.10% 7.60% 1.02% 1.27% NA
Temperate Japonica  767 70.40% 29.50% 0.13% 0.00% NA
Tropical Japonica  504 82.90% 16.90% 0.20% 0.00% NA
Japonica Intermediate  241 66.00% 33.20% 0.83% 0.00% NA
VI/Aromatic  96 78.10% 21.90% 0.00% 0.00% NA
Intermediate  90 85.60% 12.20% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0224673406 T -> DEL N N silent_mutation Average:79.897; most accessible tissue: Minghui63 panicle, score: 89.175 N N N N
vg0224673406 T -> C LOC_Os02g40700.1 upstream_gene_variant ; 2957.0bp to feature; MODIFIER silent_mutation Average:79.897; most accessible tissue: Minghui63 panicle, score: 89.175 N N N N
vg0224673406 T -> C LOC_Os02g40680.1 downstream_gene_variant ; 2614.0bp to feature; MODIFIER silent_mutation Average:79.897; most accessible tissue: Minghui63 panicle, score: 89.175 N N N N
vg0224673406 T -> C LOC_Os02g40690.1 downstream_gene_variant ; 1452.0bp to feature; MODIFIER silent_mutation Average:79.897; most accessible tissue: Minghui63 panicle, score: 89.175 N N N N
vg0224673406 T -> C LOC_Os02g40690-LOC_Os02g40700 intergenic_region ; MODIFIER silent_mutation Average:79.897; most accessible tissue: Minghui63 panicle, score: 89.175 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)
vg0224673406 T C -0.01 -0.01 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224673406 NA 5.23E-06 mr1872 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
vg0224673406 1.60E-07 4.97E-09 mr1910 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