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Detailed information for vg0717125826:

Variant ID: vg0717125826 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 17125826
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, C: 0.03, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:


CTTGTGGTAAAACTTAAGCATAAGGTGCACCTTAAGCTAATGCTACTTTCCACAATGTATATGGCTCACTTTACAAGTACAATTATTACCTTAAAATCAT[A/C]
TTTTTCATACATTATGGTTGCCCTTAGGAAACCTATAAAGGTTGGCACCCTGGGCGGCTTCCGGGGCGTACCACGTCGGATTACTGTAGCGACAGAAATA

Reverse complement sequence

TATTTCTGTCGCTACAGTAATCCGACGTGGTACGCCCCGGAAGCCGCCCAGGGTGCCAACCTTTATAGGTTTCCTAAGGGCAACCATAATGTATGAAAAA[T/G]
ATGATTTTAAGGTAATAATTGTACTTGTAAAGTGAGCCATATACATTGTGGAAAGTAGCATTAGCTTAAGGTGCACCTTATGCTTAAGTTTTACCACAAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 81.20% 14.40% 2.45% 1.93% NA
All Indica  2759 77.50% 22.00% 0.47% 0.07% NA
All Japonica  1512 94.60% 3.60% 0.00% 1.79% NA
Aus  269 36.10% 3.00% 38.29% 22.68% NA
Indica I  595 55.10% 44.40% 0.50% 0.00% NA
Indica II  465 95.30% 3.40% 1.29% 0.00% NA
Indica III  913 82.70% 17.30% 0.00% 0.00% NA
Indica Intermediate  786 77.90% 21.40% 0.51% 0.25% NA
Temperate Japonica  767 92.70% 7.20% 0.00% 0.13% NA
Tropical Japonica  504 96.60% 0.00% 0.00% 3.37% NA
Japonica Intermediate  241 96.30% 0.00% 0.00% 3.73% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 87.80% 11.10% 0.00% 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
vg0717125826 A -> DEL N N silent_mutation Average:99.341; most accessible tissue: Minghui63 panicle, score: 99.707 N N N N
vg0717125826 A -> C LOC_Os07g29224.1 upstream_gene_variant ; 376.0bp to feature; MODIFIER silent_mutation Average:99.341; most accessible tissue: Minghui63 panicle, score: 99.707 N N N N
vg0717125826 A -> C LOC_Os07g29220-LOC_Os07g29224 intergenic_region ; MODIFIER silent_mutation Average:99.341; most accessible tissue: Minghui63 panicle, score: 99.707 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)
vg0717125826 A C 0.0 0.01 0.0 0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0717125826 NA 2.53E-06 mr1245_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
vg0717125826 NA 3.84E-06 mr1355_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
vg0717125826 NA 5.22E-06 mr1373_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
vg0717125826 7.59E-07 3.64E-11 mr1648_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
vg0717125826 NA 2.24E-08 mr1648_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
vg0717125826 NA 1.38E-06 mr1655_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
vg0717125826 NA 6.26E-07 mr1669_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
vg0717125826 NA 4.18E-06 mr1669_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