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Detailed information for vg0919162888:

Variant ID: vg0919162888 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 19162888
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


AGATAGTGTTGAGGTAATTAGGATGATAATAAATGGTAGATAATGTTAATTGATCACATGTGGGGGTTGTGGTATCGATACGGTTAACCAAAGTAGGAAG[G/A]
TGATATGGATGCTGCTGTATAACTTTAGCTTAATCCTGCACTCAAGTTGACAACTTGTGATTGGTTAATGGTGACTGTAATTCTGTACGTCTATGATGCA

Reverse complement sequence

TGCATCATAGACGTACAGAATTACAGTCACCATTAACCAATCACAAGTTGTCAACTTGAGTGCAGGATTAAGCTAAAGTTATACAGCAGCATCCATATCA[C/T]
CTTCCTACTTTGGTTAACCGTATCGATACCACAACCCCCACATGTGATCAATTAACATTATCTACCATTTATTATCATCCTAATTACCTCAACACTATCT

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 76.40% 23.40% 0.11% 0.00% NA
All Indica  2759 60.10% 39.80% 0.18% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 98.20% 1.70% 0.17% 0.00% NA
Indica II  465 34.00% 65.80% 0.22% 0.00% NA
Indica III  913 48.60% 51.00% 0.33% 0.00% NA
Indica Intermediate  786 59.90% 40.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0919162888 G -> A LOC_Os09g32095.1 upstream_gene_variant ; 3397.0bp to feature; MODIFIER silent_mutation Average:74.974; most accessible tissue: Zhenshan97 flower, score: 91.158 N N N N
vg0919162888 G -> A LOC_Os09g32100.1 upstream_gene_variant ; 3462.0bp to feature; MODIFIER silent_mutation Average:74.974; most accessible tissue: Zhenshan97 flower, score: 91.158 N N N N
vg0919162888 G -> A LOC_Os09g32095-LOC_Os09g32100 intergenic_region ; MODIFIER silent_mutation Average:74.974; most accessible tissue: Zhenshan97 flower, score: 91.158 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)
vg0919162888 G A -0.07 -0.06 -0.07 -0.05 -0.08 -0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0919162888 NA 2.92E-06 mr1268 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
vg0919162888 NA 2.72E-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
vg0919162888 NA 2.67E-08 mr1465 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
vg0919162888 NA 1.82E-07 mr1542 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
vg0919162888 NA 8.63E-08 mr1607 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
vg0919162888 NA 3.94E-09 mr1608 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
vg0919162888 NA 2.41E-10 mr1720 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
vg0919162888 NA 4.43E-09 mr1174_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
vg0919162888 NA 8.11E-08 mr1527_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
vg0919162888 NA 4.11E-08 mr1557_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
vg0919162888 NA 5.93E-07 mr1842_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