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Detailed information for vg0205749844:

Variant ID: vg0205749844 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 5749844
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCAACAGCGACCTTGATAGCCAACAGAAACTAACGGATTTGGATCCGGTGCAACACCTAGTGTGAGCAGTCACACTAGGAACTTTTGATGCAAATCCAAG[G/A]
GTCTAGAATCTACAAAGTACTGTTCACATCTGAAAAAAACTGCAGAACTACTGTAGCAGCAGCACTATAGCATCAGATCTAGACCGTTCACTGGAAAAAT

Reverse complement sequence

ATTTTTCCAGTGAACGGTCTAGATCTGATGCTATAGTGCTGCTGCTACAGTAGTTCTGCAGTTTTTTTCAGATGTGAACAGTACTTTGTAGATTCTAGAC[C/T]
CTTGGATTTGCATCAAAAGTTCCTAGTGTGACTGCTCACACTAGGTGTTGCACCGGATCCAAATCCGTTAGTTTCTGTTGGCTATCAAGGTCGCTGTTGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.00% 46.60% 2.39% 0.00% NA
All Indica  2759 84.80% 11.20% 3.99% 0.00% NA
All Japonica  1512 1.50% 98.50% 0.00% 0.00% NA
Aus  269 0.40% 99.60% 0.00% 0.00% NA
Indica I  595 88.90% 9.40% 1.68% 0.00% NA
Indica II  465 94.00% 4.50% 1.51% 0.00% NA
Indica III  913 83.10% 10.30% 6.57% 0.00% NA
Indica Intermediate  786 78.40% 17.40% 4.20% 0.00% NA
Temperate Japonica  767 1.70% 98.30% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 94.80% 1.04% 0.00% NA
Intermediate  90 45.60% 52.20% 2.22% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0205749844 G -> A LOC_Os02g10820.1 upstream_gene_variant ; 1703.0bp to feature; MODIFIER silent_mutation Average:96.153; most accessible tissue: Zhenshan97 flag leaf, score: 97.563 N N N N
vg0205749844 G -> A LOC_Os02g10830.1 upstream_gene_variant ; 344.0bp to feature; MODIFIER silent_mutation Average:96.153; most accessible tissue: Zhenshan97 flag leaf, score: 97.563 N N N N
vg0205749844 G -> A LOC_Os02g10840.1 downstream_gene_variant ; 451.0bp to feature; MODIFIER silent_mutation Average:96.153; most accessible tissue: Zhenshan97 flag leaf, score: 97.563 N N N N
vg0205749844 G -> A LOC_Os02g10840.2 downstream_gene_variant ; 451.0bp to feature; MODIFIER silent_mutation Average:96.153; most accessible tissue: Zhenshan97 flag leaf, score: 97.563 N N N N
vg0205749844 G -> A LOC_Os02g10840.3 downstream_gene_variant ; 3367.0bp to feature; MODIFIER silent_mutation Average:96.153; most accessible tissue: Zhenshan97 flag leaf, score: 97.563 N N N N
vg0205749844 G -> A LOC_Os02g10830-LOC_Os02g10840 intergenic_region ; MODIFIER silent_mutation Average:96.153; most accessible tissue: Zhenshan97 flag leaf, score: 97.563 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)
vg0205749844 G A -0.09 -0.13 -0.07 -0.13 -0.08 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0205749844 NA 9.24E-34 mr1037 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
vg0205749844 NA 1.50E-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
vg0205749844 NA 2.18E-38 mr1094 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
vg0205749844 NA 2.55E-51 mr1096 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
vg0205749844 NA 3.20E-13 mr1183 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
vg0205749844 NA 2.13E-21 mr1244 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
vg0205749844 NA 2.93E-09 mr1352 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
vg0205749844 NA 6.41E-49 mr1458 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
vg0205749844 NA 1.18E-08 mr1465 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
vg0205749844 NA 1.20E-12 mr1503 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
vg0205749844 NA 5.69E-11 mr1720 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
vg0205749844 NA 5.36E-52 mr1798 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
vg0205749844 NA 9.16E-14 mr1807 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
vg0205749844 NA 2.17E-09 mr1929 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
vg0205749844 NA 3.20E-38 mr1037_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
vg0205749844 NA 1.68E-08 mr1037_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
vg0205749844 NA 1.57E-49 mr1063_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
vg0205749844 NA 1.34E-44 mr1094_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
vg0205749844 NA 3.23E-21 mr1164_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
vg0205749844 NA 1.48E-15 mr1180_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
vg0205749844 NA 2.08E-20 mr1183_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
vg0205749844 NA 2.00E-18 mr1457_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
vg0205749844 NA 1.27E-53 mr1458_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
vg0205749844 NA 3.44E-09 mr1649_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
vg0205749844 NA 2.98E-16 mr1720_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
vg0205749844 NA 1.05E-71 mr1798_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