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Detailed information for vg0313767191:

Variant ID: vg0313767191 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 13767191
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


AAAGATGAGAGCAAGTACAATAGCAAGCTATTAACTAGTTGTAAACATATTTTAATGAGATAAAGGATGAGAGAGAAGAGCAGCGGGCTACATATCTGTA[G/A]
CTAGCTGCAGCGCGGACTCCAATACAAGATGTGTGTATGACAGGTGGGACCATATATTAATACTATAGTAAGTAACTATTGTATGAATTGGCTATTAGAT

Reverse complement sequence

ATCTAATAGCCAATTCATACAATAGTTACTTACTATAGTATTAATATATGGTCCCACCTGTCATACACACATCTTGTATTGGAGTCCGCGCTGCAGCTAG[C/T]
TACAGATATGTAGCCCGCTGCTCTTCTCTCTCATCCTTTATCTCATTAAAATATGTTTACAACTAGTTAATAGCTTGCTATTGTACTTGCTCTCATCTTT

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 97.30% 2.70% 0.00% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 96.80% 3.20% 0.00% 0.00% NA
Aus  269 73.60% 26.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 96.00% 4.00% 0.00% 0.00% NA
Tropical Japonica  504 97.00% 3.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0313767191 G -> A LOC_Os03g24200.1 downstream_gene_variant ; 2311.0bp to feature; MODIFIER silent_mutation Average:80.966; most accessible tissue: Minghui63 panicle, score: 93.176 N N N N
vg0313767191 G -> A LOC_Os03g24210.1 intron_variant ; MODIFIER silent_mutation Average:80.966; most accessible tissue: Minghui63 panicle, score: 93.176 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)
vg0313767191 G A -0.02 -0.03 -0.02 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0313767191 3.30E-06 3.30E-06 mr1015_2 Jap_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
vg0313767191 1.43E-06 6.97E-09 mr1274_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
vg0313767191 3.89E-07 3.89E-07 mr1587_2 Jap_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
vg0313767191 NA 3.03E-06 mr1758_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
vg0313767191 NA 2.68E-06 mr1792_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