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Detailed information for vg0805565693:

Variant ID: vg0805565693 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 5565693
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:


CCGCGGCTTGCGTGTTTCGGGTACGGTTATGGGCCGCTGGGGATGGCGACGTTGCACCAGCTGCGACACCTGTTTAGTTCAACGCGTAGTTTGGATTTTG[G/A]
TTGAAATTGGAGATGATGTGACTGAAAAGTTGTGTGTGTATGACATGTTAATGTGATGGAAAAAGACTGAAATTTAGATCCAAATTTTGGATCTAAACAC

Reverse complement sequence

GTGTTTAGATCCAAAATTTGGATCTAAATTTCAGTCTTTTTCCATCACATTAACATGTCATACACACACAACTTTTCAGTCACATCATCTCCAATTTCAA[C/T]
CAAAATCCAAACTACGCGTTGAACTAAACAGGTGTCGCAGCTGGTGCAACGTCGCCATCCCCAGCGGCCCATAACCGTACCCGAAACACGCAAGCCGCGG

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 62.00% 18.70% 2.33% 17.03% NA
All Indica  2759 58.90% 17.40% 3.01% 20.70% NA
All Japonica  1512 61.50% 26.30% 1.72% 10.52% NA
Aus  269 98.90% 0.00% 0.00% 1.12% NA
Indica I  595 31.10% 42.20% 6.72% 20.00% NA
Indica II  465 55.70% 9.90% 3.44% 30.97% NA
Indica III  913 79.00% 6.00% 0.00% 15.01% NA
Indica Intermediate  786 58.40% 16.40% 3.44% 21.76% NA
Temperate Japonica  767 57.60% 38.10% 1.30% 3.00% NA
Tropical Japonica  504 73.20% 5.40% 1.59% 19.84% NA
Japonica Intermediate  241 49.40% 32.40% 3.32% 14.94% NA
VI/Aromatic  96 42.70% 2.10% 0.00% 55.21% NA
Intermediate  90 74.40% 3.30% 1.11% 21.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0805565693 G -> A LOC_Os08g09610.1 upstream_gene_variant ; 1269.0bp to feature; MODIFIER silent_mutation Average:93.713; most accessible tissue: Minghui63 young leaf, score: 97.529 N N N N
vg0805565693 G -> A LOC_Os08g09610-LOC_Os08g09630 intergenic_region ; MODIFIER silent_mutation Average:93.713; most accessible tissue: Minghui63 young leaf, score: 97.529 N N N N
vg0805565693 G -> DEL N N silent_mutation Average:93.713; most accessible tissue: Minghui63 young leaf, score: 97.529 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)
vg0805565693 G A 0.01 -0.04 -0.02 0.02 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0805565693 NA 2.89E-15 Heading_date 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
vg0805565693 NA 4.15E-06 mr1020 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
vg0805565693 NA 3.22E-07 mr1038 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
vg0805565693 NA 3.92E-07 mr1389 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
vg0805565693 NA 3.26E-06 mr1405 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
vg0805565693 NA 3.55E-06 mr1729 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
vg0805565693 NA 9.41E-06 mr1851 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
vg0805565693 1.63E-07 2.91E-09 mr1897 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
vg0805565693 NA 2.45E-06 mr1125_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
vg0805565693 NA 1.98E-06 mr1318_2 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
vg0805565693 NA 6.88E-06 mr1359_2 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
vg0805565693 NA 2.66E-06 mr1359_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
vg0805565693 NA 9.77E-06 mr1456_2 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
vg0805565693 NA 2.40E-07 mr1585_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
vg0805565693 5.97E-07 5.97E-07 mr1608_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
vg0805565693 NA 1.25E-07 mr1729_2 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
vg0805565693 NA 4.02E-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
vg0805565693 NA 3.44E-07 mr1788_2 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
vg0805565693 NA 1.84E-06 mr1807_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