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Detailed information for vg0603271543:

Variant ID: vg0603271543 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 3271543
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGATTCCATGCATGTCTTCTTCAAGCAATCTACACCAACACGTCGTTCAAGACTGACGAGGCTAGACGACGGGGGCGGGCGAAGCCGACGCGAAGGCTAC[G/A]
TCACCAATATCGGCGCACGGACCGACGAGGCCGTGGACCGCTGCCGGCGCCCACATCTACATCACCATCACAACCATGCATGGAGAATGCGAAACGAAGA

Reverse complement sequence

TCTTCGTTTCGCATTCTCCATGCATGGTTGTGATGGTGATGTAGATGTGGGCGCCGGCAGCGGTCCACGGCCTCGTCGGTCCGTGCGCCGATATTGGTGA[C/T]
GTAGCCTTCGCGTCGGCTTCGCCCGCCCCCGTCGTCTAGCCTCGTCAGTCTTGAACGACGTGTTGGTGTAGATTGCTTGAAGAAGACATGCATGGAATCG

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 91.90% 8.00% 0.02% 0.00% NA
All Indica  2759 93.40% 6.50% 0.04% 0.00% NA
All Japonica  1512 99.40% 0.60% 0.00% 0.00% NA
Aus  269 32.30% 67.70% 0.00% 0.00% NA
Indica I  595 93.30% 6.60% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 83.30% 16.70% 0.00% 0.00% NA
Temperate Japonica  767 99.20% 0.80% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0603271543 G -> A LOC_Os06g06880.1 upstream_gene_variant ; 4235.0bp to feature; MODIFIER silent_mutation Average:79.375; most accessible tissue: Zhenshan97 panicle, score: 89.389 N N N N
vg0603271543 G -> A LOC_Os06g06900.1 upstream_gene_variant ; 1830.0bp to feature; MODIFIER silent_mutation Average:79.375; most accessible tissue: Zhenshan97 panicle, score: 89.389 N N N N
vg0603271543 G -> A LOC_Os06g06890.1 downstream_gene_variant ; 109.0bp to feature; MODIFIER silent_mutation Average:79.375; most accessible tissue: Zhenshan97 panicle, score: 89.389 N N N N
vg0603271543 G -> A LOC_Os06g06890-LOC_Os06g06900 intergenic_region ; MODIFIER silent_mutation Average:79.375; most accessible tissue: Zhenshan97 panicle, score: 89.389 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)
vg0603271543 G A 0.0 0.07 0.07 -0.01 0.08 0.1

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0603271543 NA 6.89E-07 mr1125 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
vg0603271543 7.90E-06 NA mr1970 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
vg0603271543 NA 3.54E-07 mr1125_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
vg0603271543 NA 4.49E-06 mr1702_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