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Detailed information for vg1122503059:

Variant ID: vg1122503059 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 22503059
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


GATGATCAAACATATCTTAAAAAAATCAATGGCGTCATATATTAAAAAACAGAGGTAGTATGACACTGTAATGGTCCGTATACCTTATATCAGTATATAT[G/A]
ATGTAGTGATATTATCTAAAAGGTCTATAAAAATTCCTGGAAATGGATAATCTGCGACTACTAGGTTCTAAAATTCCTCCTGAAATGTTCTACGAGTTAG

Reverse complement sequence

CTAACTCGTAGAACATTTCAGGAGGAATTTTAGAACCTAGTAGTCGCAGATTATCCATTTCCAGGAATTTTTATAGACCTTTTAGATAATATCACTACAT[C/T]
ATATATACTGATATAAGGTATACGGACCATTACAGTGTCATACTACCTCTGTTTTTTAATATATGACGCCATTGATTTTTTTAAGATATGTTTGATCATC

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 59.90% 39.90% 0.15% 0.02% NA
All Indica  2759 42.40% 57.30% 0.25% 0.04% NA
All Japonica  1512 97.20% 2.80% 0.00% 0.00% NA
Aus  269 21.90% 78.10% 0.00% 0.00% NA
Indica I  595 20.20% 79.50% 0.34% 0.00% NA
Indica II  465 50.30% 49.20% 0.22% 0.22% NA
Indica III  913 52.40% 47.40% 0.22% 0.00% NA
Indica Intermediate  786 42.90% 56.90% 0.25% 0.00% NA
Temperate Japonica  767 96.20% 3.80% 0.00% 0.00% NA
Tropical Japonica  504 98.00% 2.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 85.40% 14.60% 0.00% 0.00% NA
Intermediate  90 60.00% 40.00% 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
vg1122503059 G -> A LOC_Os11g37950.1 3_prime_UTR_variant ; 356.0bp to feature; MODIFIER silent_mutation Average:67.674; most accessible tissue: Zhenshan97 root, score: 88.628 N N N N
vg1122503059 G -> A LOC_Os11g37944.1 upstream_gene_variant ; 1865.0bp to feature; MODIFIER silent_mutation Average:67.674; most accessible tissue: Zhenshan97 root, score: 88.628 N N N N
vg1122503059 G -> A LOC_Os11g37960.1 upstream_gene_variant ; 2934.0bp to feature; MODIFIER silent_mutation Average:67.674; most accessible tissue: Zhenshan97 root, score: 88.628 N N N N
vg1122503059 G -> A LOC_Os11g37940.1 downstream_gene_variant ; 2568.0bp to feature; MODIFIER silent_mutation Average:67.674; most accessible tissue: Zhenshan97 root, score: 88.628 N N N N
vg1122503059 G -> DEL N N silent_mutation Average:67.674; most accessible tissue: Zhenshan97 root, score: 88.628 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)
vg1122503059 G A 0.07 -0.04 -0.03 -0.03 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1122503059 NA 4.77E-06 mr1066 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
vg1122503059 NA 1.42E-09 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
vg1122503059 NA 3.10E-06 mr1215 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
vg1122503059 NA 1.25E-08 mr1275 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
vg1122503059 NA 5.52E-10 mr1307 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
vg1122503059 NA 2.40E-07 mr1315 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
vg1122503059 NA 4.10E-07 mr1392 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
vg1122503059 NA 1.54E-06 mr1420 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
vg1122503059 NA 2.01E-08 mr1488 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
vg1122503059 3.04E-06 3.02E-06 mr1497 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
vg1122503059 NA 7.27E-08 mr1506 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
vg1122503059 NA 9.88E-07 mr1511 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
vg1122503059 NA 6.02E-08 mr1514 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
vg1122503059 NA 3.50E-07 mr1680 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
vg1122503059 NA 2.18E-07 mr1810 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
vg1122503059 NA 4.93E-08 mr1886 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
vg1122503059 NA 4.72E-08 mr1979 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
vg1122503059 NA 8.07E-12 mr1986 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