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Detailed information for vg1103096922:

Variant ID: vg1103096922 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 3096922
Reference Allele: CAlternative Allele: T,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.70, A: 0.30, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:


TGTACAAATATAAAAAATAAAAAGTTGTGCTTAAAGTGCTTTGGATAATAAAGTAAGTCACAAATAAAATAAATAATAATTCCAAATTTTTTTAATAAGA[C/T,A]
GAATGGTCAAACAGTGTAAGTAGAAAGTTAAAATTTGTTATATTATGGGACGGATGGAGTAACACAGCGCTTCCGTAACTCGCAATTTGCAAACGATTTT

Reverse complement sequence

AAAATCGTTTGCAAATTGCGAGTTACGGAAGCGCTGTGTTACTCCATCCGTCCCATAATATAACAAATTTTAACTTTCTACTTACACTGTTTGACCATTC[G/A,T]
TCTTATTAAAAAAATTTGGAATTATTATTTATTTTATTTGTGACTTACTTTATTATCCAAAGCACTTTAAGCACAACTTTTTATTTTTTATATTTGTACA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.30% 35.90% 0.08% 0.00% A: 1.69%
All Indica  2759 39.90% 59.30% 0.11% 0.00% A: 0.72%
All Japonica  1512 95.60% 1.40% 0.07% 0.00% A: 2.91%
Aus  269 89.60% 7.10% 0.00% 0.00% A: 3.35%
Indica I  595 90.30% 9.60% 0.17% 0.00% NA
Indica II  465 11.40% 88.40% 0.22% 0.00% NA
Indica III  913 23.30% 75.00% 0.00% 0.00% A: 1.64%
Indica Intermediate  786 37.90% 61.30% 0.13% 0.00% A: 0.64%
Temperate Japonica  767 98.80% 1.00% 0.13% 0.00% NA
Tropical Japonica  504 89.50% 2.40% 0.00% 0.00% A: 8.13%
Japonica Intermediate  241 98.30% 0.40% 0.00% 0.00% A: 1.24%
VI/Aromatic  96 93.80% 1.00% 0.00% 0.00% A: 5.21%
Intermediate  90 73.30% 24.40% 0.00% 0.00% A: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1103096922 C -> T LOC_Os11g06420.1 upstream_gene_variant ; 1542.0bp to feature; MODIFIER silent_mutation Average:88.403; most accessible tissue: Minghui63 panicle, score: 97.671 N N N N
vg1103096922 C -> T LOC_Os11g06420.2 upstream_gene_variant ; 1542.0bp to feature; MODIFIER silent_mutation Average:88.403; most accessible tissue: Minghui63 panicle, score: 97.671 N N N N
vg1103096922 C -> T LOC_Os11g06410.1 downstream_gene_variant ; 599.0bp to feature; MODIFIER silent_mutation Average:88.403; most accessible tissue: Minghui63 panicle, score: 97.671 N N N N
vg1103096922 C -> T LOC_Os11g06410.3 downstream_gene_variant ; 599.0bp to feature; MODIFIER silent_mutation Average:88.403; most accessible tissue: Minghui63 panicle, score: 97.671 N N N N
vg1103096922 C -> T LOC_Os11g06410.2 downstream_gene_variant ; 599.0bp to feature; MODIFIER silent_mutation Average:88.403; most accessible tissue: Minghui63 panicle, score: 97.671 N N N N
vg1103096922 C -> T LOC_Os11g06410-LOC_Os11g06420 intergenic_region ; MODIFIER silent_mutation Average:88.403; most accessible tissue: Minghui63 panicle, score: 97.671 N N N N
vg1103096922 C -> A LOC_Os11g06420.1 upstream_gene_variant ; 1542.0bp to feature; MODIFIER silent_mutation Average:88.403; most accessible tissue: Minghui63 panicle, score: 97.671 N N N N
vg1103096922 C -> A LOC_Os11g06420.2 upstream_gene_variant ; 1542.0bp to feature; MODIFIER silent_mutation Average:88.403; most accessible tissue: Minghui63 panicle, score: 97.671 N N N N
vg1103096922 C -> A LOC_Os11g06410.1 downstream_gene_variant ; 599.0bp to feature; MODIFIER silent_mutation Average:88.403; most accessible tissue: Minghui63 panicle, score: 97.671 N N N N
vg1103096922 C -> A LOC_Os11g06410.3 downstream_gene_variant ; 599.0bp to feature; MODIFIER silent_mutation Average:88.403; most accessible tissue: Minghui63 panicle, score: 97.671 N N N N
vg1103096922 C -> A LOC_Os11g06410.2 downstream_gene_variant ; 599.0bp to feature; MODIFIER silent_mutation Average:88.403; most accessible tissue: Minghui63 panicle, score: 97.671 N N N N
vg1103096922 C -> A LOC_Os11g06410-LOC_Os11g06420 intergenic_region ; MODIFIER silent_mutation Average:88.403; most accessible tissue: Minghui63 panicle, score: 97.671 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)
vg1103096922 C A 0.01 0.02 0.01 -0.01 0.0 0.01
vg1103096922 C T 0.01 0.03 0.02 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1103096922 NA 2.24E-06 mr1030 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
vg1103096922 NA 3.67E-06 mr1749 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
vg1103096922 NA 2.00E-10 mr1794 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
vg1103096922 NA 1.82E-06 mr1904 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
vg1103096922 NA 1.18E-07 mr1184_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
vg1103096922 NA 1.87E-06 mr1186_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
vg1103096922 NA 5.13E-07 mr1245_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
vg1103096922 NA 7.18E-06 mr1245_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
vg1103096922 NA 2.15E-07 mr1278_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
vg1103096922 NA 7.78E-07 mr1293_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
vg1103096922 NA 9.93E-07 mr1294_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
vg1103096922 NA 2.17E-06 mr1321_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
vg1103096922 NA 4.64E-09 mr1322_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
vg1103096922 NA 8.46E-07 mr1329_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
vg1103096922 NA 2.53E-13 mr1330_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
vg1103096922 NA 2.85E-07 mr1332_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
vg1103096922 NA 1.70E-06 mr1336_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
vg1103096922 NA 2.93E-13 mr1338_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
vg1103096922 NA 4.25E-08 mr1338_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
vg1103096922 NA 3.28E-06 mr1355_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
vg1103096922 NA 2.43E-07 mr1360_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
vg1103096922 NA 1.31E-08 mr1360_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
vg1103096922 NA 1.29E-08 mr1373_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
vg1103096922 NA 1.02E-06 mr1373_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
vg1103096922 NA 5.43E-06 mr1420_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
vg1103096922 NA 2.16E-06 mr1428_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
vg1103096922 NA 5.36E-06 mr1445_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
vg1103096922 NA 2.40E-06 mr1445_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
vg1103096922 NA 1.25E-11 mr1449_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
vg1103096922 NA 2.14E-06 mr1449_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
vg1103096922 NA 2.19E-06 mr1488_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
vg1103096922 NA 1.27E-06 mr1492_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
vg1103096922 NA 6.03E-08 mr1497_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
vg1103096922 NA 5.00E-07 mr1497_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
vg1103096922 NA 4.56E-09 mr1508_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
vg1103096922 NA 2.15E-07 mr1508_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
vg1103096922 NA 2.29E-06 mr1524_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
vg1103096922 NA 5.29E-09 mr1565_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
vg1103096922 NA 2.78E-14 mr1579_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
vg1103096922 NA 5.12E-06 mr1579_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
vg1103096922 NA 7.84E-06 mr1647_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
vg1103096922 NA 1.57E-06 mr1648_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
vg1103096922 NA 1.50E-06 mr1655_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
vg1103096922 5.55E-06 2.61E-07 mr1657_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
vg1103096922 NA 5.85E-06 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
vg1103096922 NA 4.00E-08 mr1683_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
vg1103096922 NA 2.79E-10 mr1690_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
vg1103096922 NA 4.58E-14 mr1715_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
vg1103096922 NA 1.09E-06 mr1756_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
vg1103096922 NA 4.26E-07 mr1779_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
vg1103096922 NA 6.76E-19 mr1794_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
vg1103096922 NA 1.24E-11 mr1794_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
vg1103096922 NA 1.92E-09 mr1851_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
vg1103096922 NA 6.05E-10 mr1861_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
vg1103096922 NA 2.82E-06 mr1895_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
vg1103096922 NA 3.04E-07 mr1992_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