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Detailed information for vg0203129511:

Variant ID: vg0203129511 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 3129511
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.04, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


GCAATGCCCATTTGCTACCGATGGTTAGTTTCAGAAGAACTTTGCTACCGATGGTCCTTGTTCATTGATTGCGCAGAAAGTAATACCGATGACTATGTTA[T/C]
CCCGTGCCTGTCCAATTGTTGCATTGGTTCAGACAACTGTGACGACCGCTGTTTCAAGCTTGACAATTGACAAAACTATGAAAAATCCTGGTCGCCTCCT

Reverse complement sequence

AGGAGGCGACCAGGATTTTTCATAGTTTTGTCAATTGTCAAGCTTGAAACAGCGGTCGTCACAGTTGTCTGAACCAATGCAACAATTGGACAGGCACGGG[A/G]
TAACATAGTCATCGGTATTACTTTCTGCGCAATCAATGAACAAGGACCATCGGTAGCAAAGTTCTTCTGAAACTAACCATCGGTAGCAAATGGGCATTGC

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 50.70% 46.60% 2.31% 0.40% NA
All Indica  2759 34.00% 62.80% 2.50% 0.69% NA
All Japonica  1512 85.80% 13.90% 0.26% 0.00% NA
Aus  269 17.10% 82.50% 0.37% 0.00% NA
Indica I  595 53.30% 46.70% 0.00% 0.00% NA
Indica II  465 52.00% 47.70% 0.22% 0.00% NA
Indica III  913 10.00% 83.90% 4.05% 2.08% NA
Indica Intermediate  786 36.50% 59.50% 3.94% 0.00% NA
Temperate Japonica  767 75.60% 24.30% 0.13% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 91.70% 7.10% 1.24% 0.00% NA
VI/Aromatic  96 63.50% 6.20% 30.21% 0.00% NA
Intermediate  90 61.10% 32.20% 6.67% 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
vg0203129511 T -> DEL N N silent_mutation Average:66.625; most accessible tissue: Callus, score: 89.715 N N N N
vg0203129511 T -> C LOC_Os02g06250.1 upstream_gene_variant ; 2849.0bp to feature; MODIFIER silent_mutation Average:66.625; most accessible tissue: Callus, score: 89.715 N N N N
vg0203129511 T -> C LOC_Os02g06260.1 upstream_gene_variant ; 255.0bp to feature; MODIFIER silent_mutation Average:66.625; most accessible tissue: Callus, score: 89.715 N N N N
vg0203129511 T -> C LOC_Os02g06270.1 downstream_gene_variant ; 3264.0bp to feature; MODIFIER silent_mutation Average:66.625; most accessible tissue: Callus, score: 89.715 N N N N
vg0203129511 T -> C LOC_Os02g06260-LOC_Os02g06270 intergenic_region ; MODIFIER silent_mutation Average:66.625; most accessible tissue: Callus, score: 89.715 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)
vg0203129511 T C -0.02 0.04 0.03 0.02 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0203129511 NA 7.16E-06 mr1452_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
vg0203129511 NA 6.66E-06 mr1511_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
vg0203129511 NA 3.46E-12 mr1582_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
vg0203129511 NA 5.54E-08 mr1582_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