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Detailed information for vg1121732413:

Variant ID: vg1121732413 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 21732413
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


TGAAGTTCATCCTTTGGTGAAGGTGGAGGAAGGCATAGCTGCTGAGGCAAAACTCTGGGAACTACATAGCACATGTTTTGGTGTATAGCCTGACGGCACA[G/A]
ATCCATAATCTCCTCTCTGCTGCACATCTCCATCTGGAGCAGAGCGTCTCGTAGCAGATCAATCGCTTGTGCAGGAATACTGGCAGAGGTGCAATCTCTT

Reverse complement sequence

AAGAGATTGCACCTCTGCCAGTATTCCTGCACAAGCGATTGATCTGCTACGAGACGCTCTGCTCCAGATGGAGATGTGCAGCAGAGAGGAGATTATGGAT[C/T]
TGTGCCGTCAGGCTATACACCAAAACATGTGCTATGTAGTTCCCAGAGTTTTGCCTCAGCAGCTATGCCTTCCTCCACCTTCACCAAAGGATGAACTTCA

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 87.70% 12.10% 0.21% 0.00% NA
All Indica  2759 83.20% 16.60% 0.25% 0.00% NA
All Japonica  1512 98.60% 1.40% 0.00% 0.00% NA
Aus  269 89.20% 10.40% 0.37% 0.00% NA
Indica I  595 81.20% 18.70% 0.17% 0.00% NA
Indica II  465 77.20% 22.40% 0.43% 0.00% NA
Indica III  913 88.20% 11.80% 0.00% 0.00% NA
Indica Intermediate  786 82.40% 17.00% 0.51% 0.00% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 42.70% 56.20% 1.04% 0.00% NA
Intermediate  90 87.80% 11.10% 1.11% 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
vg1121732413 G -> A LOC_Os11g36830.1 5_prime_UTR_premature_start_codon_gain_variant ; LOW silent_mutation Average:61.999; most accessible tissue: Minghui63 flower, score: 89.589 N N N N
vg1121732413 G -> A LOC_Os11g36830.1 5_prime_UTR_variant ; 447.0bp to feature; MODIFIER silent_mutation Average:61.999; most accessible tissue: Minghui63 flower, score: 89.589 N N N N
vg1121732413 G -> A LOC_Os11g36810.1 upstream_gene_variant ; 3204.0bp to feature; MODIFIER silent_mutation Average:61.999; most accessible tissue: Minghui63 flower, score: 89.589 N N N N
vg1121732413 G -> A LOC_Os11g36800.1 downstream_gene_variant ; 4773.0bp to feature; MODIFIER silent_mutation Average:61.999; most accessible tissue: Minghui63 flower, score: 89.589 N N N N
vg1121732413 G -> A LOC_Os11g36820.1 downstream_gene_variant ; 1830.0bp to feature; MODIFIER silent_mutation Average:61.999; most accessible tissue: Minghui63 flower, score: 89.589 N N N N
vg1121732413 G -> A LOC_Os11g36840.1 downstream_gene_variant ; 1764.0bp to feature; MODIFIER silent_mutation Average:61.999; most accessible tissue: Minghui63 flower, score: 89.589 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)
vg1121732413 G A -0.01 -0.02 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1121732413 1.11E-06 NA mr1008_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