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Detailed information for vg1012224763:

Variant ID: vg1012224763 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 12224763
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


TCTCTTTCTCGGTCGCTTGTTCGCATCAGGTTGCGTTGCCCCGAGTCCCCGACGCCGCATCAGCTATCGGTACTCCCCGTAAAAAAAAGGTTATCGCTAT[G/T]
AGCTGAGCTCGCGTATCAGCTTGTCGTTGCAAGTTGAGCTGTTTAGACGCATAATCCGCATGAGCTATCCTGTCTCAGATTTCGTACCGGTGATATTTGA

Reverse complement sequence

TCAAATATCACCGGTACGAAATCTGAGACAGGATAGCTCATGCGGATTATGCGTCTAAACAGCTCAACTTGCAACGACAAGCTGATACGCGAGCTCAGCT[C/A]
ATAGCGATAACCTTTTTTTTACGGGGAGTACCGATAGCTGATGCGGCGTCGGGGACTCGGGGCAACGCAACCTGATGCGAACAAGCGACCGAGAAAGAGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.10% 2.50% 0.87% 2.50% NA
All Indica  2759 97.50% 0.50% 0.58% 1.49% NA
All Japonica  1512 97.60% 0.10% 0.00% 2.31% NA
Aus  269 38.30% 37.50% 9.29% 14.87% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 94.60% 0.90% 0.99% 3.50% NA
Indica Intermediate  786 97.50% 0.50% 0.89% 1.15% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% NA
Tropical Japonica  504 94.80% 0.00% 0.00% 5.16% NA
Japonica Intermediate  241 96.30% 0.40% 0.00% 3.32% NA
VI/Aromatic  96 97.90% 1.00% 0.00% 1.04% NA
Intermediate  90 95.60% 3.30% 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
vg1012224763 G -> T LOC_Os10g23840.1 upstream_gene_variant ; 206.0bp to feature; MODIFIER silent_mutation Average:73.566; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 N N N N
vg1012224763 G -> T LOC_Os10g23830.1 downstream_gene_variant ; 383.0bp to feature; MODIFIER silent_mutation Average:73.566; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 N N N N
vg1012224763 G -> T LOC_Os10g23830-LOC_Os10g23840 intergenic_region ; MODIFIER silent_mutation Average:73.566; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 N N N N
vg1012224763 G -> DEL N N silent_mutation Average:73.566; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 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)
vg1012224763 G T 0.24 0.05 0.04 0.07 0.1 0.1

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1012224763 NA 3.35E-06 mr1006 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
vg1012224763 NA 4.28E-06 mr1007 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
vg1012224763 4.47E-06 NA mr1010 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
vg1012224763 NA 2.77E-06 mr1052 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
vg1012224763 NA 4.07E-09 mr1317 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
vg1012224763 NA 6.25E-11 mr1612 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
vg1012224763 NA 7.26E-14 mr1897 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
vg1012224763 NA 3.77E-10 mr1927 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
vg1012224763 NA 3.39E-08 mr1989 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