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Detailed information for vg0807746311:

Variant ID: vg0807746311 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 7746311
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.03, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


TCATGCCAAGGGTTCCTTGCTACAATAAAACAAAAGCAAATGCAGATGATGAATTAGCAGTGGAAACCTCATAACAAAAGAACCTTGGAAGTGCACGTAG[A/G]
GTGCACCATTCCAGTACTCCGCACGTATAAATCGCGGTCCCCAAGACATCATGTCTGGTGAATCCAACAGCACCTCTAATGATGTCCCTGCCATGTTGGT

Reverse complement sequence

ACCAACATGGCAGGGACATCATTAGAGGTGCTGTTGGATTCACCAGACATGATGTCTTGGGGACCGCGATTTATACGTGCGGAGTACTGGAATGGTGCAC[T/C]
CTACGTGCACTTCCAAGGTTCTTTTGTTATGAGGTTTCCACTGCTAATTCATCATCTGCATTTGCTTTTGTTTTATTGTAGCAAGGAACCCTTGGCATGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.20% 6.80% 0.02% 0.00% NA
All Indica  2759 93.90% 6.00% 0.04% 0.00% NA
All Japonica  1512 90.30% 9.70% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 72.70% 27.10% 0.22% 0.00% NA
Indica III  913 98.80% 1.20% 0.00% 0.00% NA
Indica Intermediate  786 96.30% 3.70% 0.00% 0.00% NA
Temperate Japonica  767 85.50% 14.50% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 86.70% 13.30% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0807746311 A -> G LOC_Os08g13050.1 missense_variant ; p.Leu185Pro; MODERATE nonsynonymous_codon ; L185P Average:71.638; most accessible tissue: Zhenshan97 panicle, score: 89.623 unknown unknown DELETERIOUS 0.00

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)
vg0807746311 A G 0.01 0.01 0.01 0.0 -0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0807746311 3.46E-06 3.46E-06 mr1542_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
vg0807746311 NA 1.49E-06 mr1865_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
vg0807746311 2.15E-08 2.15E-08 mr1973_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