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Detailed information for vg0706400044:

Variant ID: vg0706400044 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 6400044
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


ATGCGGCTAAAGCGTCGGCCACCTTATTACATTCACGTGGGCAATAACCAACACGGAAAGAAAGAAAAGCCAAAGCAATAAACTTCTTCATTTGCAGGAC[G/C]
AAGCCACCTAACGCTGCAAGATGGATGTTGCTCTCCTTCAGGGCTTGGACAAGCAACAGCGAGTCCGTCTCCAAGTGAATATGCGCTATACCCCACTGTG

Reverse complement sequence

CACAGTGGGGTATAGCGCATATTCACTTGGAGACGGACTCGCTGTTGCTTGTCCAAGCCCTGAAGGAGAGCAACATCCATCTTGCAGCGTTAGGTGGCTT[C/G]
GTCCTGCAAATGAAGAAGTTTATTGCTTTGGCTTTTCTTTCTTTCCGTGTTGGTTATTGCCCACGTGAATGTAATAAGGTGGCCGACGCTTTAGCCGCAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 72.50% 16.70% 2.07% 8.78% NA
All Indica  2759 84.60% 2.80% 2.36% 10.33% NA
All Japonica  1512 53.00% 43.90% 0.26% 2.78% NA
Aus  269 83.60% 3.70% 1.12% 11.52% NA
Indica I  595 82.20% 3.00% 3.36% 11.43% NA
Indica II  465 91.00% 3.90% 2.37% 2.80% NA
Indica III  913 84.40% 0.80% 1.53% 13.25% NA
Indica Intermediate  786 82.70% 4.20% 2.54% 10.56% NA
Temperate Japonica  767 44.90% 50.60% 0.26% 4.30% NA
Tropical Japonica  504 80.80% 18.10% 0.00% 1.19% NA
Japonica Intermediate  241 21.20% 76.80% 0.83% 1.24% NA
VI/Aromatic  96 10.40% 18.80% 25.00% 45.83% NA
Intermediate  90 61.10% 22.20% 2.22% 14.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0706400044 G -> DEL N N silent_mutation Average:81.46; most accessible tissue: Zhenshan97 flower, score: 95.349 N N N N
vg0706400044 G -> C LOC_Os07g11590.1 upstream_gene_variant ; 4527.0bp to feature; MODIFIER silent_mutation Average:81.46; most accessible tissue: Zhenshan97 flower, score: 95.349 N N N N
vg0706400044 G -> C LOC_Os07g11600.1 upstream_gene_variant ; 1806.0bp to feature; MODIFIER silent_mutation Average:81.46; most accessible tissue: Zhenshan97 flower, score: 95.349 N N N N
vg0706400044 G -> C LOC_Os07g11590-LOC_Os07g11600 intergenic_region ; MODIFIER silent_mutation Average:81.46; most accessible tissue: Zhenshan97 flower, score: 95.349 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)
vg0706400044 G C 0.0 0.02 -0.02 0.07 0.09 0.1

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0706400044 NA 3.90E-08 mr1097 Jap_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
vg0706400044 NA 2.13E-06 mr1154 Jap_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
vg0706400044 NA 9.97E-08 mr1252 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
vg0706400044 NA 7.91E-06 mr1768_2 Jap_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