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Detailed information for vg1105906134:

Variant ID: vg1105906134 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5906134
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGAGTTTAAGATTTAAAAAAACGGTTTGGTAGTCAGCTTTTAAAAATACGGAGAAGTTGGTAATTTTTTAGATTCTACAACTATATTTTAGCATAATCT[G/T]
AGTAAAAAACCTGTCAAAACTCCCCAAATAAACCCTTAGGGCCCCTTTGAATCAAAGGATTTATGTAGGAATTTCATAGGATTCAAATCCTATAGGAAAT

Reverse complement sequence

ATTTCCTATAGGATTTGAATCCTATGAAATTCCTACATAAATCCTTTGATTCAAAGGGGCCCTAAGGGTTTATTTGGGGAGTTTTGACAGGTTTTTTACT[C/A]
AGATTATGCTAAAATATAGTTGTAGAATCTAAAAAATTACCAACTTCTCCGTATTTTTAAAAGCTGACTACCAAACCGTTTTTTTAAATCTTAAACTCCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.20% 14.30% 13.90% 8.61% NA
All Indica  2759 45.80% 19.10% 21.64% 13.45% NA
All Japonica  1512 98.40% 0.30% 0.60% 0.66% NA
Aus  269 30.10% 46.80% 15.99% 7.06% NA
Indica I  595 30.60% 24.90% 33.61% 10.92% NA
Indica II  465 46.50% 3.40% 30.32% 19.78% NA
Indica III  913 52.10% 25.00% 9.86% 13.03% NA
Indica Intermediate  786 49.50% 17.30% 21.12% 12.09% NA
Temperate Japonica  767 98.80% 0.10% 0.52% 0.52% NA
Tropical Japonica  504 97.40% 0.80% 0.99% 0.79% NA
Japonica Intermediate  241 99.20% 0.00% 0.00% 0.83% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 68.90% 14.40% 8.89% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1105906134 G -> T LOC_Os11g10750.1 upstream_gene_variant ; 3441.0bp to feature; MODIFIER silent_mutation Average:70.533; most accessible tissue: Zhenshan97 flag leaf, score: 90.298 N N N N
vg1105906134 G -> T LOC_Os11g10760.1 downstream_gene_variant ; 1816.0bp to feature; MODIFIER silent_mutation Average:70.533; most accessible tissue: Zhenshan97 flag leaf, score: 90.298 N N N N
vg1105906134 G -> T LOC_Os11g10750-LOC_Os11g10760 intergenic_region ; MODIFIER silent_mutation Average:70.533; most accessible tissue: Zhenshan97 flag leaf, score: 90.298 N N N N
vg1105906134 G -> DEL N N silent_mutation Average:70.533; most accessible tissue: Zhenshan97 flag leaf, score: 90.298 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)
vg1105906134 G T -0.01 -0.01 -0.01 -0.03 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105906134 NA 1.55E-06 mr1042 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
vg1105906134 NA 3.47E-09 mr1042 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
vg1105906134 NA 1.25E-06 mr1043 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
vg1105906134 2.10E-06 1.11E-09 mr1043 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
vg1105906134 NA 7.05E-06 mr1192 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
vg1105906134 NA 8.09E-08 mr1912 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
vg1105906134 1.23E-06 4.10E-08 mr1043_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
vg1105906134 NA 1.33E-06 mr1180_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
vg1105906134 NA 4.20E-08 mr1378_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
vg1105906134 NA 3.66E-06 mr1743_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