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Detailed information for vg0107081316:

Variant ID: vg0107081316 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 7081316
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


GGGTATACATGTCTTTTTACGAGTGAATTGACACTGTTAACTGATGATAACAGAATAGGGGTAAACTGAAGCTTCGTTTGAGAAAAGTAAGGGCAAAAAT[A/G]
CACCCTAAAAAAGGAGTAAAATCATAATTAGAATACAAAGTAGGGGTAAGTACACAATTACCCGAAAAATTTTGTTTCTGAATCTCCTGAGCAAAGTACG

Reverse complement sequence

CGTACTTTGCTCAGGAGATTCAGAAACAAAATTTTTCGGGTAATTGTGTACTTACCCCTACTTTGTATTCTAATTATGATTTTACTCCTTTTTTAGGGTG[T/C]
ATTTTTGCCCTTACTTTTCTCAAACGAAGCTTCAGTTTACCCCTATTCTGTTATCATCAGTTAACAGTGTCAATTCACTCGTAAAAAGACATGTATACCC

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 57.20% 42.50% 0.06% 0.28% NA
All Indica  2759 68.80% 30.60% 0.07% 0.47% NA
All Japonica  1512 27.40% 72.50% 0.07% 0.00% NA
Aus  269 97.40% 2.60% 0.00% 0.00% NA
Indica I  595 90.10% 9.70% 0.00% 0.17% NA
Indica II  465 63.40% 36.60% 0.00% 0.00% NA
Indica III  913 63.10% 36.00% 0.11% 0.77% NA
Indica Intermediate  786 62.60% 36.60% 0.13% 0.64% NA
Temperate Japonica  767 4.00% 95.80% 0.13% 0.00% NA
Tropical Japonica  504 67.90% 32.10% 0.00% 0.00% NA
Japonica Intermediate  241 17.40% 82.60% 0.00% 0.00% NA
VI/Aromatic  96 71.90% 28.10% 0.00% 0.00% NA
Intermediate  90 63.30% 36.70% 0.00% 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
vg0107081316 A -> G LOC_Os01g12780.1 upstream_gene_variant ; 4539.0bp to feature; MODIFIER silent_mutation Average:76.511; most accessible tissue: Zhenshan97 root, score: 87.466 N N N N
vg0107081316 A -> G LOC_Os01g12800.1 downstream_gene_variant ; 4526.0bp to feature; MODIFIER silent_mutation Average:76.511; most accessible tissue: Zhenshan97 root, score: 87.466 N N N N
vg0107081316 A -> G LOC_Os01g12790.1 intron_variant ; MODIFIER silent_mutation Average:76.511; most accessible tissue: Zhenshan97 root, score: 87.466 N N N N
vg0107081316 A -> DEL N N silent_mutation Average:76.511; most accessible tissue: Zhenshan97 root, score: 87.466 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)
vg0107081316 A G 0.0 -0.02 -0.04 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0107081316 NA 2.04E-07 mr1364 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
vg0107081316 NA 1.51E-08 mr1422 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
vg0107081316 NA 1.72E-07 mr1443 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
vg0107081316 NA 4.01E-08 mr1518 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
vg0107081316 NA 1.72E-08 mr1676 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
vg0107081316 9.28E-15 NA mr1699 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
vg0107081316 NA 1.26E-06 mr1699 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
vg0107081316 4.74E-08 2.54E-32 mr1699 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
vg0107081316 NA 2.04E-16 mr1769 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
vg0107081316 NA 2.88E-06 mr1422_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
vg0107081316 NA 1.48E-07 mr1498_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
vg0107081316 NA 3.23E-10 mr1676_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
vg0107081316 4.08E-15 NA mr1699_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
vg0107081316 2.15E-07 8.74E-12 mr1699_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
vg0107081316 2.00E-07 3.24E-25 mr1699_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
vg0107081316 NA 1.78E-08 mr1746_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
vg0107081316 NA 2.29E-08 mr1769_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
vg0107081316 NA 6.39E-15 mr1769_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
vg0107081316 NA 1.81E-11 mr1993_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