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Detailed information for vg0315993749:

Variant ID: vg0315993749 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 15993749
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


TGTTTTTGGCTAAAAATTTTTTGATCTAAACAAGGCCTAAGAGCAAGTATAATATTAAGCTATAAGCCTACTATAAGCTTATGTGGAGGAAAGATATAAC[A/G]
AAAGGTCAAGGATGTTGGCTCTCATGCAAGAGCTAGCTTAACACAAGCTCCTAGGTAAATACATTAAATGTATAGGTGAGAGAGGAAAAGAAAATTGTAG

Reverse complement sequence

CTACAATTTTCTTTTCCTCTCTCACCTATACATTTAATGTATTTACCTAGGAGCTTGTGTTAAGCTAGCTCTTGCATGAGAGCCAACATCCTTGACCTTT[T/C]
GTTATATCTTTCCTCCACATAAGCTTATAGTAGGCTTATAGCTTAATATTATACTTGCTCTTAGGCCTTGTTTAGATCAAAAAATTTTTAGCCAAAAACA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.90% 11.80% 4.42% 12.89% NA
All Indica  2759 60.20% 19.30% 7.00% 13.48% NA
All Japonica  1512 86.50% 0.50% 0.93% 12.10% NA
Aus  269 84.40% 0.00% 0.00% 15.61% NA
Indica I  595 74.80% 0.20% 13.28% 11.76% NA
Indica II  465 28.00% 57.20% 9.03% 5.81% NA
Indica III  913 68.30% 11.00% 1.53% 19.17% NA
Indica Intermediate  786 58.90% 21.00% 7.38% 12.72% NA
Temperate Japonica  767 99.10% 0.30% 0.39% 0.26% NA
Tropical Japonica  504 63.70% 0.60% 1.59% 34.13% NA
Japonica Intermediate  241 94.20% 0.80% 1.24% 3.73% NA
VI/Aromatic  96 91.70% 3.10% 0.00% 5.21% NA
Intermediate  90 71.10% 18.90% 2.22% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0315993749 A -> DEL N N silent_mutation Average:71.283; most accessible tissue: Minghui63 panicle, score: 92.078 N N N N
vg0315993749 A -> G LOC_Os03g27840.1 downstream_gene_variant ; 914.0bp to feature; MODIFIER silent_mutation Average:71.283; most accessible tissue: Minghui63 panicle, score: 92.078 N N N N
vg0315993749 A -> G LOC_Os03g27840-LOC_Os03g27850 intergenic_region ; MODIFIER silent_mutation Average:71.283; most accessible tissue: Minghui63 panicle, score: 92.078 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)
vg0315993749 A G 0.0 0.04 0.02 0.01 0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0315993749 NA 4.00E-18 Grain_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
vg0315993749 NA 1.86E-16 Grain_length Ind_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
vg0315993749 NA 1.85E-06 mr1050 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
vg0315993749 NA 2.83E-08 mr1272 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
vg0315993749 NA 1.97E-06 mr1291 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
vg0315993749 NA 3.91E-06 mr1502 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
vg0315993749 NA 1.86E-06 mr1892 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
vg0315993749 NA 2.36E-09 mr1935 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
vg0315993749 NA 1.24E-07 mr1050_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
vg0315993749 NA 3.96E-06 mr1272_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
vg0315993749 NA 1.44E-06 mr1291_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
vg0315993749 NA 6.97E-06 mr1354_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
vg0315993749 NA 3.01E-06 mr1542_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
vg0315993749 NA 3.95E-06 mr1892_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
vg0315993749 NA 1.82E-06 mr1942_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