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Detailed information for vg1208788061:

Variant ID: vg1208788061 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 8788061
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


CGGGTGGTGATGCATGTGCTTCTACAATCATGTATTGGTTAATTGGGTGCATGCATGTATGTTCTATAGGCTTCTGGGTGCTCACCGAGATGCTAGACAA[G/A,T]
GCTGGGGATGTCTGTAGAGTCACAGCGACGGCGAAGCTCCATGGCGGCATGGCACAACTCCAGGGATGACGTCCGCTGCTCGATCTGTAAGGGGAGTCAC

Reverse complement sequence

GTGACTCCCCTTACAGATCGAGCAGCGGACGTCATCCCTGGAGTTGTGCCATGCCGCCATGGAGCTTCGCCGTCGCTGTGACTCTACAGACATCCCCAGC[C/T,A]
TTGTCTAGCATCTCGGTGAGCACCCAGAAGCCTATAGAACATACATGCATGCACCCAATTAACCAATACATGATTGTAGAAGCACATGCATCACCACCCG

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 88.00% 8.00% 1.29% 2.75% NA
All Indica  2759 80.70% 13.40% 2.21% 3.62% NA
All Japonica  1512 97.90% 0.10% 0.00% 1.92% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 92.40% 3.40% 2.86% 1.34% NA
Indica II  465 68.60% 21.90% 1.94% 7.53% NA
Indica III  913 81.20% 14.50% 1.10% 3.29% NA
Indica Intermediate  786 78.50% 14.90% 3.18% 3.44% NA
Temperate Japonica  767 96.10% 0.10% 0.00% 3.78% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 4.40% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1208788061 G -> DEL LOC_Os12g15390.1 N frameshift_variant Average:62.826; most accessible tissue: Minghui63 flag leaf, score: 83.197 N N N N
vg1208788061 G -> A LOC_Os12g15390.1 synonymous_variant ; p.Lys67Lys; LOW synonymous_codon Average:62.826; most accessible tissue: Minghui63 flag leaf, score: 83.197 N N N N
vg1208788061 G -> T LOC_Os12g15390.1 missense_variant ; p.Lys67Asn; MODERATE N Average:62.826; most accessible tissue: Minghui63 flag leaf, score: 83.197 N N N N
vg1208788061 G -> T LOC_Os12g15400.1 upstream_gene_variant ; 4253.0bp to feature; MODIFIER N Average:62.826; most accessible tissue: Minghui63 flag leaf, score: 83.197 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)
vg1208788061 G A -0.02 -0.02 -0.03 -0.03 -0.03 -0.03
vg1208788061 G T -0.05 -0.03 -0.06 -0.04 -0.06 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1208788061 8.57E-07 NA mr1242_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
vg1208788061 NA 8.83E-06 mr1308_2 Ind_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
vg1208788061 7.79E-06 7.78E-06 mr1853_2 Ind_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