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Detailed information for vg0334733128:

Variant ID: vg0334733128 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 34733128
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTGTTAATTAGTAGATGATGATGTGACATCTTGTTAGTGGATGATGATGTGACATCTTTGCATGTTAAGTTTAAAGAGTTAGTCGGAGATAACTTTATA[G/A]
TAAGATAGATAAGCCAAATGACGGGGGGCCTTTGCAAACAGACTGAAGTTATCTCCGTACACGTACGCGCAAGGAAGAGACTGGTGGACCCAAAAGGCCC

Reverse complement sequence

GGGCCTTTTGGGTCCACCAGTCTCTTCCTTGCGCGTACGTGTACGGAGATAACTTCAGTCTGTTTGCAAAGGCCCCCCGTCATTTGGCTTATCTATCTTA[C/T]
TATAAAGTTATCTCCGACTAACTCTTTAAACTTAACATGCAAAGATGTCACATCATCATCCACTAACAAGATGTCACATCATCATCTACTAATTAACAAG

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 89.70% 10.20% 0.04% 0.00% NA
All Indica  2759 82.90% 17.00% 0.07% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 97.10% 2.70% 0.17% 0.00% NA
Indica II  465 91.00% 9.00% 0.00% 0.00% NA
Indica III  913 68.70% 31.30% 0.00% 0.00% NA
Indica Intermediate  786 84.00% 15.90% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0334733128 G -> A LOC_Os03g61140.1 upstream_gene_variant ; 1595.0bp to feature; MODIFIER silent_mutation Average:94.072; most accessible tissue: Minghui63 panicle, score: 98.67 N N N N
vg0334733128 G -> A LOC_Os03g61140.2 upstream_gene_variant ; 1597.0bp to feature; MODIFIER silent_mutation Average:94.072; most accessible tissue: Minghui63 panicle, score: 98.67 N N N N
vg0334733128 G -> A LOC_Os03g61150.1 downstream_gene_variant ; 325.0bp to feature; MODIFIER silent_mutation Average:94.072; most accessible tissue: Minghui63 panicle, score: 98.67 N N N N
vg0334733128 G -> A LOC_Os03g61150.2 downstream_gene_variant ; 325.0bp to feature; MODIFIER silent_mutation Average:94.072; most accessible tissue: Minghui63 panicle, score: 98.67 N N N N
vg0334733128 G -> A LOC_Os03g61150.3 downstream_gene_variant ; 343.0bp to feature; MODIFIER silent_mutation Average:94.072; most accessible tissue: Minghui63 panicle, score: 98.67 N N N N
vg0334733128 G -> A LOC_Os03g61140-LOC_Os03g61150 intergenic_region ; MODIFIER silent_mutation Average:94.072; most accessible tissue: Minghui63 panicle, score: 98.67 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)
vg0334733128 G A -0.02 -0.07 -0.07 -0.08 -0.08 -0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0334733128 NA 3.26E-10 Heading_date Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0334733128 NA 9.52E-08 mr1305 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
vg0334733128 NA 3.22E-06 mr1586 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
vg0334733128 1.82E-06 1.46E-07 mr1305_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
vg0334733128 NA 6.95E-06 mr1409_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
vg0334733128 3.78E-06 NA mr1765_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
vg0334733128 1.04E-06 1.04E-06 mr1765_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