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Detailed information for vg0713666866:

Variant ID: vg0713666866 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 13666866
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTCTGACCGGCGACCCCGAGCGGTCTGACCGGCCCTATATGGCTAGTCCGGCCGGTTCTGGGCAGAGCTCTAGGGGGCACGTTTCAGTCAATTTGGAAG[C/A]
CGAATTGATTGTGAATTCGAATGTTTGTGCCCAGGAGATAGAAGAGGATTGGAGAATTCCTTTCATTCGATATTTGAAAGATCCCACACTTAAGGTTGAT

Reverse complement sequence

ATCAACCTTAAGTGTGGGATCTTTCAAATATCGAATGAAAGGAATTCTCCAATCCTCTTCTATCTCCTGGGCACAAACATTCGAATTCACAATCAATTCG[G/T]
CTTCCAAATTGACTGAAACGTGCCCCCTAGAGCTCTGCCCAGAACCGGCCGGACTAGCCATATAGGGCCGGTCAGACCGCTCGGGGTCGCCGGTCAGACC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.60% 1.10% 0.21% 1.12% NA
All Indica  2759 97.80% 1.80% 0.33% 0.04% NA
All Japonica  1512 99.70% 0.00% 0.00% 0.26% NA
Aus  269 99.30% 0.00% 0.00% 0.74% NA
Indica I  595 93.40% 5.40% 1.18% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 98.10% 1.50% 0.25% 0.13% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.00% 0.00% 0.40% NA
Japonica Intermediate  241 99.20% 0.00% 0.00% 0.83% NA
VI/Aromatic  96 53.10% 0.00% 1.04% 45.83% NA
Intermediate  90 96.70% 1.10% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0713666866 C -> DEL N N silent_mutation Average:59.603; most accessible tissue: Minghui63 flag leaf, score: 82.975 N N N N
vg0713666866 C -> A LOC_Os07g24100.1 intron_variant ; MODIFIER silent_mutation Average:59.603; most accessible tissue: Minghui63 flag leaf, score: 82.975 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)
vg0713666866 C A -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
vg0713666866 NA 8.39E-06 mr1579 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
vg0713666866 1.78E-06 5.07E-07 mr1701 Ind_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