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Detailed information for vg1120800949:

Variant ID: vg1120800949 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 20800949
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGAGCAAACCCTGTTGCAGCGTAGCCGAGGTGCCCTGCCCACCTTCCCCTTCCGCACCGTACCATCGTCGGAGCCCGTACGCTGCCCCGCCGGAGCTGCC[A/G]
CCTTCCGTACGTGCGCTGCGCCAGAGTTGCTGCCCCTTGATCGAGCCGCCGCCTTCCCGTTCCCGTGGTGCTGCGACAGACTCGCCGCTGGCTCGCCGCT

Reverse complement sequence

AGCGGCGAGCCAGCGGCGAGTCTGTCGCAGCACCACGGGAACGGGAAGGCGGCGGCTCGATCAAGGGGCAGCAACTCTGGCGCAGCGCACGTACGGAAGG[T/C]
GGCAGCTCCGGCGGGGCAGCGTACGGGCTCCGACGATGGTACGGTGCGGAAGGGGAAGGTGGGCAGGGCACCTCGGCTACGCTGCAACAGGGTTTGCTCT

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 63.20% 35.80% 0.02% 0.93% NA
All Indica  2759 93.70% 5.30% 0.04% 1.01% NA
All Japonica  1512 9.50% 90.40% 0.00% 0.13% NA
Aus  269 74.00% 20.80% 0.00% 5.20% NA
Indica I  595 83.00% 17.00% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 96.10% 1.20% 0.00% 2.74% NA
Indica Intermediate  786 95.90% 3.60% 0.13% 0.38% NA
Temperate Japonica  767 7.20% 92.80% 0.00% 0.00% NA
Tropical Japonica  504 15.30% 84.70% 0.00% 0.00% NA
Japonica Intermediate  241 4.60% 94.60% 0.00% 0.83% NA
VI/Aromatic  96 15.60% 84.40% 0.00% 0.00% NA
Intermediate  90 50.00% 50.00% 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
vg1120800949 A -> DEL N N silent_mutation Average:72.474; most accessible tissue: Zhenshan97 young leaf, score: 88.387 N N N N
vg1120800949 A -> G LOC_Os11g35500.1 upstream_gene_variant ; 1975.0bp to feature; MODIFIER silent_mutation Average:72.474; most accessible tissue: Zhenshan97 young leaf, score: 88.387 N N N N
vg1120800949 A -> G LOC_Os11g35490.1 downstream_gene_variant ; 1510.0bp to feature; MODIFIER silent_mutation Average:72.474; most accessible tissue: Zhenshan97 young leaf, score: 88.387 N N N N
vg1120800949 A -> G LOC_Os11g35490-LOC_Os11g35500 intergenic_region ; MODIFIER silent_mutation Average:72.474; most accessible tissue: Zhenshan97 young leaf, score: 88.387 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)
vg1120800949 A G 0.0 0.0 0.0 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1120800949 NA 7.83E-09 mr1776 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
vg1120800949 1.15E-06 9.69E-09 mr1758_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