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Detailed information for vg0919859957:

Variant ID: vg0919859957 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 19859957
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCCACAATATGATAAAATACTAGGTAGTAAGCATTAAATTTTCTCTTGTTACCTACCATAAACATTGTGAGTCAGTGGCGTAGTTAGCTAGGTGGCATT[G/A]
TGGTCCATGGACCACATAAAAATTTGATTGAGATTAAAACTATAGTATATGTGCTAGTTAATATAATAAAAATTGTATATTGGACCACCTATTTAATTGG

Reverse complement sequence

CCAATTAAATAGGTGGTCCAATATACAATTTTTATTATATTAACTAGCACATATACTATAGTTTTAATCTCAATCAAATTTTTATGTGGTCCATGGACCA[C/T]
AATGCCACCTAGCTAACTACGCCACTGACTCACAATGTTTATGGTAGGTAACAAGAGAAAATTTAATGCTTACTACCTAGTATTTTATCATATTGTGGAT

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 63.80% 35.10% 0.99% 0.11% NA
All Indica  2759 41.60% 56.60% 1.63% 0.18% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 71.00% 28.60% 0.37% 0.00% NA
Indica I  595 10.10% 85.20% 4.71% 0.00% NA
Indica II  465 69.50% 30.30% 0.22% 0.00% NA
Indica III  913 40.60% 58.10% 0.77% 0.55% NA
Indica Intermediate  786 50.00% 48.90% 1.15% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 83.30% 15.60% 1.11% 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
vg0919859957 G -> DEL N N silent_mutation Average:74.716; most accessible tissue: Zhenshan97 panicle, score: 98.337 N N N N
vg0919859957 G -> A LOC_Os09g33620.1 upstream_gene_variant ; 2572.0bp to feature; MODIFIER silent_mutation Average:74.716; most accessible tissue: Zhenshan97 panicle, score: 98.337 N N N N
vg0919859957 G -> A LOC_Os09g33630.1 upstream_gene_variant ; 3227.0bp to feature; MODIFIER silent_mutation Average:74.716; most accessible tissue: Zhenshan97 panicle, score: 98.337 N N N N
vg0919859957 G -> A LOC_Os09g33630.3 upstream_gene_variant ; 3227.0bp to feature; MODIFIER silent_mutation Average:74.716; most accessible tissue: Zhenshan97 panicle, score: 98.337 N N N N
vg0919859957 G -> A LOC_Os09g33630.2 upstream_gene_variant ; 3227.0bp to feature; MODIFIER silent_mutation Average:74.716; most accessible tissue: Zhenshan97 panicle, score: 98.337 N N N N
vg0919859957 G -> A LOC_Os09g33620-LOC_Os09g33630 intergenic_region ; MODIFIER silent_mutation Average:74.716; most accessible tissue: Zhenshan97 panicle, score: 98.337 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)
vg0919859957 G A -0.07 -0.06 -0.08 -0.07 -0.1 -0.11

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0919859957 NA 2.13E-06 mr1029 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
vg0919859957 NA 5.36E-15 mr1059 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
vg0919859957 NA 1.37E-15 mr1167 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
vg0919859957 NA 6.51E-07 mr1189 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
vg0919859957 4.34E-09 4.03E-10 mr1216 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
vg0919859957 6.12E-11 1.49E-17 mr1216 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
vg0919859957 NA 4.10E-11 mr1325 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
vg0919859957 NA 3.00E-06 mr1346 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
vg0919859957 NA 1.78E-10 mr1399 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
vg0919859957 NA 8.02E-06 mr1532 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
vg0919859957 NA 5.81E-15 mr1535 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
vg0919859957 NA 5.55E-20 mr1598 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
vg0919859957 NA 5.34E-06 mr1625 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
vg0919859957 NA 7.58E-06 mr1734 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
vg0919859957 NA 6.75E-08 mr1796 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
vg0919859957 NA 1.81E-06 mr1950 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
vg0919859957 NA 9.72E-10 mr1990 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
vg0919859957 NA 1.43E-06 mr1246_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
vg0919859957 NA 4.65E-08 mr1299_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
vg0919859957 NA 1.40E-32 mr1598_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
vg0919859957 NA 6.56E-06 mr1648_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
vg0919859957 NA 8.90E-06 mr1655_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
vg0919859957 NA 2.43E-09 mr1676_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
vg0919859957 NA 3.32E-08 mr1700_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
vg0919859957 NA 1.82E-08 mr1970_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
vg0919859957 NA 2.38E-07 mr1973_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