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Detailed information for vg1109421335:

Variant ID: vg1109421335 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 9421335
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGTTCTGGGCGAGAGTAAGGTCATCGATCAGCCAGTCGACACGATGTCCTTGTGCGAGACGCATGTGCTGAGTGGGAGGTGGGCAGAAGCGTGGCAACT[T/C]
ACTCGCGGTGAGCCAGAGACACGGCGTAGGTTGGCGCTGGTGTCCCTTGAGGACCAGGTTGGGAGGCACGACCAGGGGGACAGGGGGTCGGCGAGGATCA

Reverse complement sequence

TGATCCTCGCCGACCCCCTGTCCCCCTGGTCGTGCCTCCCAACCTGGTCCTCAAGGGACACCAGCGCCAACCTACGCCGTGTCTCTGGCTCACCGCGAGT[A/G]
AGTTGCCACGCTTCTGCCCACCTCCCACTCAGCACATGCGTCTCGCACAAGGACATCGTGTCGACTGGCTGATCGATGACCTTACTCTCGCCCAGAACGC

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 60.20% 39.20% 0.00% 0.61% NA
All Indica  2759 95.80% 3.70% 0.00% 0.58% NA
All Japonica  1512 3.70% 95.80% 0.00% 0.53% NA
Aus  269 10.00% 89.60% 0.00% 0.37% NA
Indica I  595 93.80% 3.50% 0.00% 2.69% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 97.00% 3.00% 0.00% 0.00% NA
Indica Intermediate  786 93.80% 6.20% 0.00% 0.00% NA
Temperate Japonica  767 3.40% 96.60% 0.00% 0.00% NA
Tropical Japonica  504 3.60% 94.80% 0.00% 1.59% NA
Japonica Intermediate  241 5.00% 95.00% 0.00% 0.00% NA
VI/Aromatic  96 71.90% 28.10% 0.00% 0.00% NA
Intermediate  90 56.70% 38.90% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1109421335 T -> DEL N N silent_mutation Average:66.424; most accessible tissue: Zhenshan97 young leaf, score: 91.466 N N N N
vg1109421335 T -> C LOC_Os11g16990.1 upstream_gene_variant ; 3261.0bp to feature; MODIFIER silent_mutation Average:66.424; most accessible tissue: Zhenshan97 young leaf, score: 91.466 N N N N
vg1109421335 T -> C LOC_Os11g17014.1 upstream_gene_variant ; 2286.0bp to feature; MODIFIER silent_mutation Average:66.424; most accessible tissue: Zhenshan97 young leaf, score: 91.466 N N N N
vg1109421335 T -> C LOC_Os11g16990-LOC_Os11g17014 intergenic_region ; MODIFIER silent_mutation Average:66.424; most accessible tissue: Zhenshan97 young leaf, score: 91.466 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)
vg1109421335 T C -0.07 -0.02 0.0 -0.04 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1109421335 NA 2.53E-21 mr1051 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
vg1109421335 4.39E-06 NA mr1101 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
vg1109421335 NA 1.41E-47 mr1109 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
vg1109421335 NA 9.35E-15 mr1199 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
vg1109421335 NA 5.44E-29 mr1208 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
vg1109421335 NA 1.19E-17 mr1255 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
vg1109421335 NA 4.37E-07 mr1321 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
vg1109421335 NA 1.11E-25 mr1551 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
vg1109421335 NA 6.38E-18 mr1552 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
vg1109421335 NA 7.51E-28 mr1638 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
vg1109421335 5.67E-06 5.67E-06 mr1727 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
vg1109421335 NA 3.98E-32 mr1793 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
vg1109421335 NA 4.55E-25 mr1841 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
vg1109421335 NA 2.01E-18 mr1913 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
vg1109421335 NA 2.05E-15 mr1916 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
vg1109421335 3.87E-06 NA mr1150_2 Jap_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
vg1109421335 NA 3.55E-39 mr1745_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
vg1109421335 NA 1.62E-09 mr1751_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
vg1109421335 NA 4.14E-51 mr1793_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
vg1109421335 NA 3.80E-32 mr1913_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
vg1109421335 NA 1.29E-29 mr1932_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
vg1109421335 NA 6.22E-25 mr1943_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