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Detailed information for vg0142009982:

Variant ID: vg0142009982 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 42009982
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


GGAGCTCATGGAAAAAGAGGTCGTCGGAGTCGGACCCATCGGCGGCTAACGTTTTTCTTTATCTCTTTCTCTTTCTTTATTACTCCCTCCGTCTCTAAAT[G/A]
ATTTTTTTTAAAACATGTTTAATCATTTATCTTATTAAAAAATTTTGTTAATATTATTCAAAAAATTTAGTAGTATTATATTTAACAATGAATCAAATGA

Reverse complement sequence

TCATTTGATTCATTGTTAAATATAATACTACTAAATTTTTTGAATAATATTAACAAAATTTTTTAATAAGATAAATGATTAAACATGTTTTAAAAAAAAT[C/T]
ATTTAGAGACGGAGGGAGTAATAAAGAAAGAGAAAGAGATAAAGAAAAACGTTAGCCGCCGATGGGTCCGACTCCGACGACCTCTTTTTCCATGAGCTCC

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 67.20% 0.10% 15.21% 17.50% NA
All Indica  2759 51.70% 0.10% 22.18% 26.02% NA
All Japonica  1512 98.40% 0.10% 1.06% 0.40% NA
Aus  269 46.80% 0.00% 24.54% 28.62% NA
Indica I  595 64.40% 0.20% 21.18% 14.29% NA
Indica II  465 30.10% 0.20% 27.31% 42.37% NA
Indica III  913 48.50% 0.00% 23.77% 27.71% NA
Indica Intermediate  786 58.50% 0.10% 18.07% 23.28% NA
Temperate Japonica  767 99.50% 0.00% 0.39% 0.13% NA
Tropical Japonica  504 97.20% 0.40% 1.39% 0.99% NA
Japonica Intermediate  241 97.50% 0.00% 2.49% 0.00% NA
VI/Aromatic  96 70.80% 0.00% 13.54% 15.62% NA
Intermediate  90 74.40% 0.00% 13.33% 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
vg0142009982 G -> A LOC_Os01g72430.1 upstream_gene_variant ; 197.0bp to feature; MODIFIER silent_mutation Average:81.898; most accessible tissue: Zhenshan97 root, score: 95.83 N N N N
vg0142009982 G -> A LOC_Os01g72450.1 upstream_gene_variant ; 2755.0bp to feature; MODIFIER silent_mutation Average:81.898; most accessible tissue: Zhenshan97 root, score: 95.83 N N N N
vg0142009982 G -> A LOC_Os01g72440.1 downstream_gene_variant ; 1204.0bp to feature; MODIFIER silent_mutation Average:81.898; most accessible tissue: Zhenshan97 root, score: 95.83 N N N N
vg0142009982 G -> A LOC_Os01g72430-LOC_Os01g72440 intergenic_region ; MODIFIER silent_mutation Average:81.898; most accessible tissue: Zhenshan97 root, score: 95.83 N N N N
vg0142009982 G -> DEL N N silent_mutation Average:81.898; most accessible tissue: Zhenshan97 root, score: 95.83 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)
vg0142009982 G A 0.03 0.02 0.01 0.01 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0142009982 NA 1.15E-07 Spikelet_length Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0142009982 NA 1.10E-06 mr1038 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
vg0142009982 NA 4.24E-06 mr1192 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
vg0142009982 NA 7.84E-10 mr1322 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
vg0142009982 NA 2.39E-06 mr1330 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
vg0142009982 NA 1.26E-08 mr1389 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
vg0142009982 NA 3.95E-09 mr1486 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
vg0142009982 NA 1.11E-07 mr1527 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
vg0142009982 NA 4.87E-07 mr1844 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
vg0142009982 NA 3.62E-11 mr1038_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
vg0142009982 NA 3.53E-06 mr1331_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
vg0142009982 NA 4.18E-07 mr1378_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
vg0142009982 NA 2.13E-06 mr1389_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
vg0142009982 NA 2.17E-09 mr1389_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
vg0142009982 NA 7.75E-06 mr1452_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
vg0142009982 NA 6.26E-06 mr1480_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
vg0142009982 NA 1.87E-11 mr1582_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
vg0142009982 NA 6.55E-07 mr1582_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
vg0142009982 NA 7.37E-07 mr1669_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
vg0142009982 NA 6.34E-06 mr1706_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
vg0142009982 NA 1.05E-06 mr1743_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
vg0142009982 4.17E-06 4.10E-10 mr1749_2 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
vg0142009982 NA 4.14E-07 mr1749_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
vg0142009982 NA 1.67E-07 mr1821_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
vg0142009982 NA 7.82E-07 mr1860_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
vg0142009982 NA 1.07E-07 mr1968_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
vg0142009982 NA 9.29E-06 mr1974_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