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Detailed information for vg0142085781:

Variant ID: vg0142085781 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 42085781
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCTGTGGCCGCATCACAATCATCATTGACACAACCGAAAACGCCACTGAATACGGTACGAGCAAAACACAACTTGTCGCCATTCAGGCTGTGTTTTTCAC[G/A]
CTAGAATTGGAAGTTTGGTTGAAATTGGAACAATGGGATGAAAAAGTTAGAAGTTTATATGTGTAGAAAAGTTTTGATGTGATGTAAAAGTTAAAAGTTT

Reverse complement sequence

AAACTTTTAACTTTTACATCACATCAAAACTTTTCTACACATATAAACTTCTAACTTTTTCATCCCATTGTTCCAATTTCAACCAAACTTCCAATTCTAG[C/T]
GTGAAAAACACAGCCTGAATGGCGACAAGTTGTGTTTTGCTCGTACCGTATTCAGTGGCGTTTTCGGTTGTGTCAATGATGATTGTGATGCGGCCACAGG

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 90.90% 9.00% 0.02% 0.00% NA
All Indica  2759 98.30% 1.70% 0.00% 0.00% NA
All Japonica  1512 84.20% 15.80% 0.00% 0.00% NA
Aus  269 58.70% 41.30% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 97.70% 2.30% 0.00% 0.00% NA
Indica Intermediate  786 97.10% 2.90% 0.00% 0.00% NA
Temperate Japonica  767 86.40% 13.60% 0.00% 0.00% NA
Tropical Japonica  504 92.90% 7.10% 0.00% 0.00% NA
Japonica Intermediate  241 58.90% 41.10% 0.00% 0.00% NA
VI/Aromatic  96 80.20% 19.80% 0.00% 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
vg0142085781 G -> A LOC_Os01g72570.1 upstream_gene_variant ; 694.0bp to feature; MODIFIER silent_mutation Average:97.223; most accessible tissue: Callus, score: 98.415 N N N N
vg0142085781 G -> A LOC_Os01g72570.2 upstream_gene_variant ; 694.0bp to feature; MODIFIER silent_mutation Average:97.223; most accessible tissue: Callus, score: 98.415 N N N N
vg0142085781 G -> A LOC_Os01g72570.3 upstream_gene_variant ; 694.0bp to feature; MODIFIER silent_mutation Average:97.223; most accessible tissue: Callus, score: 98.415 N N N N
vg0142085781 G -> A LOC_Os01g72560.1 downstream_gene_variant ; 739.0bp to feature; MODIFIER silent_mutation Average:97.223; most accessible tissue: Callus, score: 98.415 N N N N
vg0142085781 G -> A LOC_Os01g72560-LOC_Os01g72570 intergenic_region ; MODIFIER silent_mutation Average:97.223; most accessible tissue: Callus, score: 98.415 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)
vg0142085781 G A -0.01 -0.01 -0.02 -0.01 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0142085781 4.48E-06 NA mr1835_2 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