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Detailed information for vg0106819630:

Variant ID: vg0106819630 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 6819630
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCTGGGAGCACCCGCAATGGTAAAGTAAAGTGTTATCTATAAAATATATAAAACATGTACATCTCAGCAATAGACTAGATTAATAGTAAACCACTTCAAT[G/A]
GTATGTCTACATGGGTATCTATAGCTCTCTAATCCATTGTCTCATTTTTCTTTATAGACTATCTCCAGGTTAGTAGATAGCTTTGCTCTCTCTCTTCATT

Reverse complement sequence

AATGAAGAGAGAGAGCAAAGCTATCTACTAACCTGGAGATAGTCTATAAAGAAAAATGAGACAATGGATTAGAGAGCTATAGATACCCATGTAGACATAC[C/T]
ATTGAAGTGGTTTACTATTAATCTAGTCTATTGCTGAGATGTACATGTTTTATATATTTTATAGATAACACTTTACTTTACCATTGCGGGTGCTCCCAGG

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 80.00% 19.90% 0.06% 0.00% NA
All Indica  2759 90.10% 9.90% 0.00% 0.00% NA
All Japonica  1512 57.80% 42.00% 0.20% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 89.10% 10.90% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 93.90% 6.10% 0.00% 0.00% NA
Indica Intermediate  786 80.90% 19.10% 0.00% 0.00% NA
Temperate Japonica  767 40.70% 59.10% 0.26% 0.00% NA
Tropical Japonica  504 82.70% 17.30% 0.00% 0.00% NA
Japonica Intermediate  241 60.20% 39.40% 0.41% 0.00% NA
VI/Aromatic  96 74.00% 26.00% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0106819630 G -> A LOC_Os01g12440.1 downstream_gene_variant ; 4084.0bp to feature; MODIFIER silent_mutation Average:73.342; most accessible tissue: Zhenshan97 panicle, score: 90.849 N N N N
vg0106819630 G -> A LOC_Os01g12440-LOC_Os01g12460 intergenic_region ; MODIFIER silent_mutation Average:73.342; most accessible tissue: Zhenshan97 panicle, score: 90.849 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)
vg0106819630 G A 0.02 0.05 0.04 0.02 0.03 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0106819630 4.63E-08 NA mr1050_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
vg0106819630 NA 6.04E-07 mr1549_2 Jap_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
vg0106819630 NA 8.67E-06 mr1652_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
vg0106819630 NA 5.12E-07 mr1733_2 Jap_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
vg0106819630 NA 5.18E-07 mr1757_2 Jap_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
vg0106819630 NA 1.14E-06 mr1780_2 Jap_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
vg0106819630 NA 2.49E-06 mr1982_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