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Detailed information for vg0906206648:

Variant ID: vg0906206648 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 6206648
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.61, G: 0.39, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:


TCTCTAGCTACCCCAGTGGTGGGGTTTGGAGGTGGTTGCTCTGCAATAGTGAGCGAAGGAGCACGGATCCACCGCTGCCGGGCCTCGGGAGCCCGGATCT[A/G]
CACCCTTAGGGCTTTTTCATCATCGTCGTTATCGTCGAGACCATCCTCATCGACACCACCAAGCACAACGATGATGGACAGTGCATCTGGGCTCGCAGGT

Reverse complement sequence

ACCTGCGAGCCCAGATGCACTGTCCATCATCGTTGTGCTTGGTGGTGTCGATGAGGATGGTCTCGACGATAACGACGATGATGAAAAAGCCCTAAGGGTG[T/C]
AGATCCGGGCTCCCGAGGCCCGGCAGCGGTGGATCCGTGCTCCTTCGCTCACTATTGCAGAGCAACCACCTCCAAACCCCACCACTGGGGTAGCTAGAGA

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 41.80% 29.60% 0.38% 28.23% NA
All Indica  2759 46.80% 6.60% 0.54% 46.10% NA
All Japonica  1512 22.50% 77.20% 0.00% 0.26% NA
Aus  269 98.50% 0.40% 0.00% 1.12% NA
Indica I  595 20.50% 15.00% 0.67% 63.87% NA
Indica II  465 69.00% 1.30% 0.43% 29.25% NA
Indica III  913 47.50% 3.70% 0.33% 48.41% NA
Indica Intermediate  786 52.50% 6.70% 0.76% 39.95% NA
Temperate Japonica  767 11.50% 88.40% 0.00% 0.13% NA
Tropical Japonica  504 24.00% 75.60% 0.00% 0.40% NA
Japonica Intermediate  241 54.40% 45.20% 0.00% 0.41% NA
VI/Aromatic  96 50.00% 10.40% 0.00% 39.58% NA
Intermediate  90 36.70% 41.10% 3.33% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0906206648 A -> G LOC_Os09g11200.1 upstream_gene_variant ; 2298.0bp to feature; MODIFIER silent_mutation Average:47.243; most accessible tissue: Minghui63 panicle, score: 89.444 N N N N
vg0906206648 A -> G LOC_Os09g11190.1 intron_variant ; MODIFIER silent_mutation Average:47.243; most accessible tissue: Minghui63 panicle, score: 89.444 N N N N
vg0906206648 A -> DEL N N silent_mutation Average:47.243; most accessible tissue: Minghui63 panicle, score: 89.444 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)
vg0906206648 A G 0.09 0.01 0.03 0.04 0.06 0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0906206648 NA 9.07E-06 mr1114_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
vg0906206648 9.50E-07 1.08E-06 mr1471_2 Ind_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