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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1107336514:

Variant ID: vg1107336514 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 7336514
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGGTAAAGTGGGATGCCTCACAAGGTGTCAGAGATACCACGACCTATATCAACCTAATGAATAGCAATAAGGCCATCCACAATGGGTACCTCCAAGCGT[A/G]
TCCCTGCTCACAGACGTCGCCATTCCGTCCGTTTTCCGTCGCCCAGCAGAGGGGCGCGACCCCCAGCAGAGGGGCGCGTCTCCCTCCGCTCCTTGATCGC

Reverse complement sequence

GCGATCAAGGAGCGGAGGGAGACGCGCCCCTCTGCTGGGGGTCGCGCCCCTCTGCTGGGCGACGGAAAACGGACGGAATGGCGACGTCTGTGAGCAGGGA[T/C]
ACGCTTGGAGGTACCCATTGTGGATGGCCTTATTGCTATTCATTAGGTTGATATAGGTCGTGGTATCTCTGACACCTTGTGAGGCATCCCACTTTACCAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.10% 9.20% 0.08% 16.67% NA
All Indica  2759 82.80% 11.60% 0.00% 5.58% NA
All Japonica  1512 68.80% 0.40% 0.26% 30.56% NA
Aus  269 5.60% 38.70% 0.00% 55.76% NA
Indica I  595 87.40% 8.70% 0.00% 3.87% NA
Indica II  465 97.40% 1.10% 0.00% 1.51% NA
Indica III  913 74.20% 19.40% 0.00% 6.46% NA
Indica Intermediate  786 80.80% 10.90% 0.00% 8.27% NA
Temperate Japonica  767 69.00% 0.10% 0.26% 30.64% NA
Tropical Japonica  504 62.90% 1.00% 0.40% 35.71% NA
Japonica Intermediate  241 80.50% 0.00% 0.00% 19.50% NA
VI/Aromatic  96 84.40% 0.00% 0.00% 15.62% NA
Intermediate  90 87.80% 4.40% 0.00% 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
vg1107336514 A -> DEL N N silent_mutation Average:76.697; most accessible tissue: Zhenshan97 panicle, score: 88.888 N N N N
vg1107336514 A -> G LOC_Os11g13390.1 upstream_gene_variant ; 3973.0bp to feature; MODIFIER silent_mutation Average:76.697; most accessible tissue: Zhenshan97 panicle, score: 88.888 N N N N
vg1107336514 A -> G LOC_Os11g13400.1 downstream_gene_variant ; 663.0bp to feature; MODIFIER silent_mutation Average:76.697; most accessible tissue: Zhenshan97 panicle, score: 88.888 N N N N
vg1107336514 A -> G LOC_Os11g13400-LOC_Os11g13410 intergenic_region ; MODIFIER silent_mutation Average:76.697; most accessible tissue: Zhenshan97 panicle, score: 88.888 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)
vg1107336514 A G 0.01 0.01 0.01 0.03 0.03 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1107336514 5.49E-06 NA mr1137 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
vg1107336514 7.62E-06 NA mr1285 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