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Detailed information for vg0722882681:

Variant ID: vg0722882681 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 22882681
Reference Allele: GAlternative Allele: A
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: 291. )

Flanking Sequence (100 bp) in Reference Genome:


TTGGGGGGTAGCTTAGCTCTCTGGGCTTGTCAGAATTTTGCGAGTTTGCCGCGGGATCGCGGTGTTTGCGTTGGTCCGATCGGATGCAGGTGCACTCACT[G/A]
TTGTGAATTTTAGTTTTGCAGCATCTAGTCTAGCTTATGGTCGGATAAACCCTAGTAGGCTGGTAGAACCAACCGAACCTAGTAGGCTGGTAGAATCAAC

Reverse complement sequence

GTTGATTCTACCAGCCTACTAGGTTCGGTTGGTTCTACCAGCCTACTAGGGTTTATCCGACCATAAGCTAGACTAGATGCTGCAAAACTAAAATTCACAA[C/T]
AGTGAGTGCACCTGCATCCGATCGGACCAACGCAAACACCGCGATCCCGCGGCAAACTCGCAAAATTCTGACAAGCCCAGAGAGCTAAGCTACCCCCCAA

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 90.90% 9.10% 0.00% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 73.10% 26.90% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 56.80% 43.20% 0.00% 0.00% NA
Tropical Japonica  504 97.00% 3.00% 0.00% 0.00% NA
Japonica Intermediate  241 75.10% 24.90% 0.00% 0.00% NA
VI/Aromatic  96 86.50% 13.50% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0722882681 G -> A LOC_Os07g38140.1 upstream_gene_variant ; 3372.0bp to feature; MODIFIER silent_mutation Average:93.93; most accessible tissue: Zhenshan97 flag leaf, score: 96.752 N N N N
vg0722882681 G -> A LOC_Os07g38150.1 upstream_gene_variant ; 616.0bp to feature; MODIFIER silent_mutation Average:93.93; most accessible tissue: Zhenshan97 flag leaf, score: 96.752 N N N N
vg0722882681 G -> A LOC_Os07g38160.1 intron_variant ; MODIFIER silent_mutation Average:93.93; most accessible tissue: Zhenshan97 flag leaf, score: 96.752 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)
vg0722882681 G A -0.01 -0.01 -0.02 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0722882681 6.83E-06 3.07E-17 Awn_length All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0722882681 NA 1.57E-08 Awn_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0722882681 NA 6.68E-06 mr1382 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
vg0722882681 NA 1.38E-06 mr1043_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
vg0722882681 3.95E-08 NA mr1057_2 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
vg0722882681 NA 9.69E-06 mr1185_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
vg0722882681 NA 9.27E-06 mr1263_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
vg0722882681 NA 2.56E-06 mr1680_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
vg0722882681 NA 1.31E-08 mr1757_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
vg0722882681 NA 2.78E-06 mr1780_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