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Detailed information for vg0806440451:

Variant ID: vg0806440451 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 6440451
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.55, G: 0.45, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


CATCTAGAAATTGTCGCATGGGAGGCGAAGTCCAGCAACAAGGAAGGCAGCAAAAATGACTGTTCGCCTGTCGCCTGGCGAAGGGACGGTGGCTTCGCCC[G/C]
CACAGTTCACTTGGCCCTCTGCAAGAGCACCGGAGAGGACGAACTCAGCCAAGTCAGGCTCCTTGACAAGGGACTTGCCAAGGTAGCACGACCACCCTTC

Reverse complement sequence

GAAGGGTGGTCGTGCTACCTTGGCAAGTCCCTTGTCAAGGAGCCTGACTTGGCTGAGTTCGTCCTCTCCGGTGCTCTTGCAGAGGGCCAAGTGAACTGTG[C/G]
GGGCGAAGCCACCGTCCCTTCGCCAGGCGACAGGCGAACAGTCATTTTTGCTGCCTTCCTTGTTGCTGGACTTCGCCTCCCATGCGACAATTTCTAGATG

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 43.00% 38.40% 4.36% 14.33% NA
All Indica  2759 58.00% 11.60% 7.00% 23.38% NA
All Japonica  1512 2.50% 95.60% 0.53% 1.32% NA
Aus  269 98.90% 0.40% 0.37% 0.37% NA
Indica I  595 28.60% 31.30% 8.74% 31.43% NA
Indica II  465 68.20% 11.80% 6.67% 13.33% NA
Indica III  913 65.10% 0.80% 6.68% 27.49% NA
Indica Intermediate  786 66.00% 9.30% 6.23% 18.45% NA
Temperate Japonica  767 1.80% 97.40% 0.39% 0.39% NA
Tropical Japonica  504 3.00% 92.90% 0.99% 3.17% NA
Japonica Intermediate  241 3.70% 95.90% 0.00% 0.41% NA
VI/Aromatic  96 95.80% 3.10% 1.04% 0.00% NA
Intermediate  90 37.80% 46.70% 3.33% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0806440451 G -> C LOC_Os08g10930.1 intron_variant ; MODIFIER silent_mutation Average:37.917; most accessible tissue: Minghui63 young leaf, score: 84.144 N N N N
vg0806440451 G -> DEL N N silent_mutation Average:37.917; most accessible tissue: Minghui63 young leaf, score: 84.144 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)
vg0806440451 G C -0.05 -0.03 -0.03 -0.05 -0.05 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0806440451 NA 4.31E-44 mr1194 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
vg0806440451 NA 1.47E-07 mr1004_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
vg0806440451 NA 4.72E-09 mr1379_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
vg0806440451 6.96E-06 5.70E-08 mr1567_2 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
vg0806440451 NA 4.28E-06 mr1806_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