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Detailed information for vg0206307094:

Variant ID: vg0206307094 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 6307094
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, T: 0.01, A: 0.01, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


GGCCTGTAGAGGTTGGTGAGGACATGATCGGCGAGCACGTACTTCTCGAGGGTGACGAGGATGAGACCACACCATTGCCGAAGTTGAGATCGAGGGTGAC[G/A]
GGCACGAGAGACTTGATGTTCAGCACCAAGACTGCCTGAGCGTGGAGATTGGCGGTGGCGTCGTCGTCGAGGTCGACGTTGTAGAAGTTCTAGGCGGTAG

Reverse complement sequence

CTACCGCCTAGAACTTCTACAACGTCGACCTCGACGACGACGCCACCGCCAATCTCCACGCTCAGGCAGTCTTGGTGCTGAACATCAAGTCTCTCGTGCC[C/T]
GTCACCCTCGATCTCAACTTCGGCAATGGTGTGGTCTCATCCTCGTCACCCTCGAGAAGTACGTGCTCGCCGATCATGTCCTCACCAACCTCTACAGGCC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.10% 10.10% 0.11% 3.70% NA
All Indica  2759 81.30% 16.00% 0.04% 2.68% NA
All Japonica  1512 98.50% 1.40% 0.07% 0.07% NA
Aus  269 75.80% 0.00% 0.74% 23.42% NA
Indica I  595 93.30% 6.70% 0.00% 0.00% NA
Indica II  465 65.80% 26.50% 0.22% 7.53% NA
Indica III  913 79.10% 19.20% 0.00% 1.75% NA
Indica Intermediate  786 83.80% 13.20% 0.00% 2.93% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 97.00% 3.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 1.20% 0.41% 0.41% NA
VI/Aromatic  96 56.20% 8.30% 1.04% 34.38% NA
Intermediate  90 88.90% 6.70% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0206307094 G -> A LOC_Os02g12120.1 synonymous_variant ; p.Pro284Pro; LOW synonymous_codon Average:69.284; most accessible tissue: Zhenshan97 young leaf, score: 86.852 N N N N
vg0206307094 G -> DEL LOC_Os02g12120.1 N frameshift_variant Average:69.284; most accessible tissue: Zhenshan97 young leaf, score: 86.852 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)
vg0206307094 G 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
vg0206307094 NA 6.88E-06 mr1006 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
vg0206307094 NA 3.24E-06 mr1007 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
vg0206307094 NA 7.67E-07 mr1037 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
vg0206307094 NA 5.60E-06 mr1052 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
vg0206307094 NA 1.08E-07 mr1410 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
vg0206307094 NA 2.97E-10 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
vg0206307094 NA 5.12E-08 mr1004_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