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Detailed information for vg1122503071:

Variant ID: vg1122503071 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 22503071
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, A: 0.06, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


TATCTTAAAAAAATCAATGGCGTCATATATTAAAAAACAGAGGTAGTATGACACTGTAATGGTCCGTATACCTTATATCAGTATATATGATGTAGTGATA[T/A]
TATCTAAAAGGTCTATAAAAATTCCTGGAAATGGATAATCTGCGACTACTAGGTTCTAAAATTCCTCCTGAAATGTTCTACGAGTTAGGTCGAATGCATC

Reverse complement sequence

GATGCATTCGACCTAACTCGTAGAACATTTCAGGAGGAATTTTAGAACCTAGTAGTCGCAGATTATCCATTTCCAGGAATTTTTATAGACCTTTTAGATA[A/T]
TATCACTACATCATATATACTGATATAAGGTATACGGACCATTACAGTGTCATACTACCTCTGTTTTTTAATATATGACGCCATTGATTTTTTTAAGATA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 81.50% 18.30% 0.17% 0.00% NA
All Indica  2759 73.50% 26.30% 0.22% 0.00% NA
All Japonica  1512 94.20% 5.60% 0.13% 0.00% NA
Aus  269 85.90% 14.10% 0.00% 0.00% NA
Indica I  595 86.20% 13.80% 0.00% 0.00% NA
Indica II  465 54.60% 45.20% 0.22% 0.00% NA
Indica III  913 78.60% 21.20% 0.11% 0.00% NA
Indica Intermediate  786 69.10% 30.40% 0.51% 0.00% NA
Temperate Japonica  767 95.30% 4.60% 0.13% 0.00% NA
Tropical Japonica  504 90.90% 8.90% 0.20% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 84.40% 15.60% 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
vg1122503071 T -> A LOC_Os11g37950.1 3_prime_UTR_variant ; 368.0bp to feature; MODIFIER silent_mutation Average:67.664; most accessible tissue: Zhenshan97 root, score: 88.238 N N N N
vg1122503071 T -> A LOC_Os11g37944.1 upstream_gene_variant ; 1877.0bp to feature; MODIFIER silent_mutation Average:67.664; most accessible tissue: Zhenshan97 root, score: 88.238 N N N N
vg1122503071 T -> A LOC_Os11g37960.1 upstream_gene_variant ; 2922.0bp to feature; MODIFIER silent_mutation Average:67.664; most accessible tissue: Zhenshan97 root, score: 88.238 N N N N
vg1122503071 T -> A LOC_Os11g37940.1 downstream_gene_variant ; 2580.0bp to feature; MODIFIER silent_mutation Average:67.664; most accessible tissue: Zhenshan97 root, score: 88.238 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)
vg1122503071 T A 0.01 -0.02 -0.01 -0.02 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1122503071 NA 7.19E-07 mr1170 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
vg1122503071 NA 9.85E-06 mr1500 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
vg1122503071 7.82E-06 2.07E-10 mr1524 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
vg1122503071 NA 3.21E-06 mr1821 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
vg1122503071 NA 2.02E-06 mr1974 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