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Detailed information for vg0303334757:

Variant ID: vg0303334757 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 3334757
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.71, T: 0.29, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


GCTAACGGGCGATCGATCGCCCAGCGACAAGGGTAGCGATCCATCCCCCTTCCCCCTCCCTCCCTCCACCTGCTTTCCTTTTTTGGCACCGCATTACTTT[C/T]
CTATTTTAATAAATTTATGTACATAAAGTTTATACATCTAAAGTTTATACATCTAAAGTTTATACACGTCAAGTTTACACATCTAAAGTTTAGAGACCAA

Reverse complement sequence

TTGGTCTCTAAACTTTAGATGTGTAAACTTGACGTGTATAAACTTTAGATGTATAAACTTTAGATGTATAAACTTTATGTACATAAATTTATTAAAATAG[G/A]
AAAGTAATGCGGTGCCAAAAAAGGAAAGCAGGTGGAGGGAGGGAGGGGGAAGGGGGATGGATCGCTACCCTTGTCGCTGGGCGATCGATCGCCCGTTAGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.80% 37.80% 1.10% 1.25% NA
All Indica  2759 43.40% 53.00% 1.49% 2.14% NA
All Japonica  1512 98.80% 0.60% 0.60% 0.00% NA
Aus  269 5.20% 94.80% 0.00% 0.00% NA
Indica I  595 49.70% 47.90% 1.51% 0.84% NA
Indica II  465 65.40% 33.80% 0.43% 0.43% NA
Indica III  913 32.60% 62.90% 0.88% 3.61% NA
Indica Intermediate  786 38.00% 56.70% 2.80% 2.42% NA
Temperate Japonica  767 99.20% 0.10% 0.65% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 96.70% 1.70% 1.66% 0.00% NA
VI/Aromatic  96 56.20% 42.70% 1.04% 0.00% NA
Intermediate  90 76.70% 22.20% 1.11% 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
vg0303334757 C -> T LOC_Os03g06620.1 upstream_gene_variant ; 3512.0bp to feature; MODIFIER silent_mutation Average:74.503; most accessible tissue: Minghui63 panicle, score: 92.078 N N N N
vg0303334757 C -> T LOC_Os03g06610-LOC_Os03g06620 intergenic_region ; MODIFIER silent_mutation Average:74.503; most accessible tissue: Minghui63 panicle, score: 92.078 N N N N
vg0303334757 C -> DEL N N silent_mutation Average:74.503; most accessible tissue: Minghui63 panicle, score: 92.078 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)
vg0303334757 C T 0.0 -0.01 -0.01 0.0 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0303334757 NA 2.04E-08 mr1192 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
vg0303334757 NA 5.20E-06 mr1192 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
vg0303334757 3.89E-06 NA mr1593 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
vg0303334757 6.66E-06 1.99E-09 mr1593 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
vg0303334757 NA 6.57E-08 mr1739 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
vg0303334757 NA 3.22E-09 mr1739 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
vg0303334757 NA 2.55E-09 mr1739_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