Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0625219859:

Variant ID: vg0625219859 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 25219859
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, A: 0.23, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


AGGACCCGCTAGGGTGAGGGTGGGGGCGGGAGATTTCGCCCTAAACTCCCGAACTCCTGGTCAGGGCCGGGGGTGGGGCGAAGAATGCGGGGACAGGGCC[G/A]
GGGGCATTCTACCTCCACCAGGCCCCGACTCATCCCGTTGCCATCCTATTCACGTGTCGCTATCGTCCTCACCGCTCACCCCATTGCCATCCTATTCACG

Reverse complement sequence

CGTGAATAGGATGGCAATGGGGTGAGCGGTGAGGACGATAGCGACACGTGAATAGGATGGCAACGGGATGAGTCGGGGCCTGGTGGAGGTAGAATGCCCC[C/T]
GGCCCTGTCCCCGCATTCTTCGCCCCACCCCCGGCCCTGACCAGGAGTTCGGGAGTTTAGGGCGAAATCTCCCGCCCCCACCCTCACCCTAGCGGGTCCT

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 70.20% 29.60% 0.17% 0.00% NA
All Indica  2759 58.60% 41.30% 0.14% 0.00% NA
All Japonica  1512 99.00% 0.90% 0.07% 0.00% NA
Aus  269 20.80% 78.80% 0.37% 0.00% NA
Indica I  595 28.20% 71.40% 0.34% 0.00% NA
Indica II  465 74.40% 25.60% 0.00% 0.00% NA
Indica III  913 70.00% 29.90% 0.11% 0.00% NA
Indica Intermediate  786 58.90% 41.00% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 97.20% 2.60% 0.20% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 83.30% 15.60% 1.04% 0.00% NA
Intermediate  90 77.80% 21.10% 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
vg0625219859 G -> A LOC_Os06g42000.1 downstream_gene_variant ; 4534.0bp to feature; MODIFIER silent_mutation Average:85.129; most accessible tissue: Zhenshan97 panicle, score: 95.264 N N N N
vg0625219859 G -> A LOC_Os06g42010.1 downstream_gene_variant ; 1726.0bp to feature; MODIFIER silent_mutation Average:85.129; most accessible tissue: Zhenshan97 panicle, score: 95.264 N N N N
vg0625219859 G -> A LOC_Os06g42000-LOC_Os06g42010 intergenic_region ; MODIFIER silent_mutation Average:85.129; most accessible tissue: Zhenshan97 panicle, score: 95.264 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)
vg0625219859 G A 0.0 0.0 0.0 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0625219859 NA 1.79E-11 mr1660 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