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Detailed information for vg0217411940:

Variant ID: vg0217411940 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 17411940
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


TTCATCAACCAGATGTGCATGGTCCGTGCTAGTGGTCGAGAAAAAAAAATTTACGTGCAAATATGATTTGACAGGAGGGAGAGAAAGTAGACTTATTCCA[G/C]
GAGAGGCTCATAAAAAGGTAGACTTATTCCGAGAGGCCCATAGAAACGGTGCAAGTAATATAGGTGTAAAAAGGAGAGAGAGGTGATTACATGGAAGATA

Reverse complement sequence

TATCTTCCATGTAATCACCTCTCTCTCCTTTTTACACCTATATTACTTGCACCGTTTCTATGGGCCTCTCGGAATAAGTCTACCTTTTTATGAGCCTCTC[C/G]
TGGAATAAGTCTACTTTCTCTCCCTCCTGTCAAATCATATTTGCACGTAAATTTTTTTTTCTCGACCACTAGCACGGACCATGCACATCTGGTTGATGAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.80% 20.40% 1.71% 11.09% NA
All Indica  2759 48.10% 30.90% 2.79% 18.27% NA
All Japonica  1512 97.90% 1.40% 0.07% 0.60% NA
Aus  269 70.30% 29.00% 0.74% 0.00% NA
Indica I  595 32.40% 33.90% 6.05% 27.56% NA
Indica II  465 54.80% 11.20% 3.23% 30.75% NA
Indica III  913 59.80% 39.90% 0.11% 0.22% NA
Indica Intermediate  786 42.20% 29.80% 3.18% 24.81% NA
Temperate Japonica  767 98.80% 0.30% 0.13% 0.78% NA
Tropical Japonica  504 96.20% 3.60% 0.00% 0.20% NA
Japonica Intermediate  241 98.80% 0.40% 0.00% 0.83% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 70.00% 16.70% 1.11% 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
vg0217411940 G -> DEL N N silent_mutation Average:92.933; most accessible tissue: Minghui63 panicle, score: 98.254 N N N N
vg0217411940 G -> C LOC_Os02g29300.1 upstream_gene_variant ; 760.0bp to feature; MODIFIER silent_mutation Average:92.933; most accessible tissue: Minghui63 panicle, score: 98.254 N N N N
vg0217411940 G -> C LOC_Os02g29320.1 upstream_gene_variant ; 4443.0bp to feature; MODIFIER silent_mutation Average:92.933; most accessible tissue: Minghui63 panicle, score: 98.254 N N N N
vg0217411940 G -> C LOC_Os02g29310.1 downstream_gene_variant ; 3364.0bp to feature; MODIFIER silent_mutation Average:92.933; most accessible tissue: Minghui63 panicle, score: 98.254 N N N N
vg0217411940 G -> C LOC_Os02g29300-LOC_Os02g29310 intergenic_region ; MODIFIER silent_mutation Average:92.933; most accessible tissue: Minghui63 panicle, score: 98.254 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)
vg0217411940 G C -0.01 0.0 -0.03 -0.02 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0217411940 5.99E-06 NA mr1109 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
vg0217411940 NA 1.13E-06 mr1109 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
vg0217411940 NA 9.91E-07 mr1236 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
vg0217411940 5.23E-08 NA mr1251 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
vg0217411940 1.51E-06 1.43E-08 mr1251 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
vg0217411940 7.01E-07 NA mr1255 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
vg0217411940 4.59E-06 1.22E-07 mr1255 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
vg0217411940 NA 2.38E-07 mr1257 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
vg0217411940 NA 1.43E-06 mr1423 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
vg0217411940 5.26E-06 NA mr1435 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
vg0217411940 NA 2.58E-07 mr1435 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
vg0217411940 NA 3.24E-06 mr1559 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
vg0217411940 4.35E-07 NA mr1109_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
vg0217411940 2.99E-06 NA mr1109_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
vg0217411940 NA 5.38E-06 mr1236_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
vg0217411940 NA 6.76E-08 mr1236_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
vg0217411940 NA 7.12E-07 mr1255_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
vg0217411940 NA 2.63E-07 mr1257_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
vg0217411940 NA 6.18E-06 mr1379_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
vg0217411940 NA 1.44E-07 mr1559_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