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Detailed information for vg0804771202:

Variant ID: vg0804771202 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 4771202
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, A: 0.24, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


AGCCTACGTACCCATGTACTGATGTCTAAATATGCATCACATCAACGACTTTTACTTTGGTGTTTCCTGCGTGAAAAAGAAATTCACAATTTAGGTGTGT[A/G]
TATGATTTCTTACCACGAATCTCGATAAAGTACTACCCAGATTCATCGTACGGAGGGAGTACTCCGGTATAAGGACAAGGACCGTATTGGATTCGACGAA

Reverse complement sequence

TTCGTCGAATCCAATACGGTCCTTGTCCTTATACCGGAGTACTCCCTCCGTACGATGAATCTGGGTAGTACTTTATCGAGATTCGTGGTAAGAAATCATA[T/C]
ACACACCTAAATTGTGAATTTCTTTTTCACGCAGGAAACACCAAAGTAAAAGTCGTTGATGTGATGCATATTTAGACATCAGTACATGGGTACGTAGGCT

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 58.00% 39.30% 0.13% 2.58% NA
All Indica  2759 82.00% 13.60% 0.11% 4.28% NA
All Japonica  1512 4.80% 95.10% 0.13% 0.00% NA
Aus  269 96.30% 3.70% 0.00% 0.00% NA
Indica I  595 93.60% 6.40% 0.00% 0.00% NA
Indica II  465 40.60% 37.20% 0.22% 21.94% NA
Indica III  913 93.80% 6.10% 0.00% 0.11% NA
Indica Intermediate  786 84.00% 13.90% 0.25% 1.91% NA
Temperate Japonica  767 0.80% 99.10% 0.13% 0.00% NA
Tropical Japonica  504 11.50% 88.50% 0.00% 0.00% NA
Japonica Intermediate  241 3.30% 96.30% 0.41% 0.00% NA
VI/Aromatic  96 92.70% 5.20% 0.00% 2.08% NA
Intermediate  90 63.30% 33.30% 1.11% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0804771202 A -> G LOC_Os08g08310.1 downstream_gene_variant ; 3202.0bp to feature; MODIFIER silent_mutation Average:46.847; most accessible tissue: Callus, score: 94.774 N N N N
vg0804771202 A -> G LOC_Os08g08310-LOC_Os08g08320 intergenic_region ; MODIFIER silent_mutation Average:46.847; most accessible tissue: Callus, score: 94.774 N N N N
vg0804771202 A -> DEL N N silent_mutation Average:46.847; most accessible tissue: Callus, score: 94.774 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)
vg0804771202 A G 0.03 -0.02 -0.04 0.06 0.02 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0804771202 NA 2.92E-13 mr1149 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
vg0804771202 NA 8.72E-34 mr1448_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
vg0804771202 NA 3.54E-06 mr1539_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
vg0804771202 NA 2.46E-06 mr1592_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
vg0804771202 NA 1.44E-09 mr1624_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
vg0804771202 NA 9.26E-07 mr1732_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
vg0804771202 NA 3.73E-07 mr1748_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
vg0804771202 NA 3.05E-07 mr1837_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
vg0804771202 NA 7.78E-18 mr1874_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