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Detailed information for vg0810597423:

Variant ID: vg0810597423 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 10597423
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


GACGGGGACGTCTTCCCGGTGCGCACGAGTGAGGTGGCGGACGTGGCCAAGAGGGCCACTTCCTGGTGCGCACGAGTGAGGTGGCCTGGGGTTAATCGAC[G/A]
GGGGACGTGGCGAAGAGGGGACGTTCCTGGCCTGGGGTTAATCGACGGGGACGTCTTTCCGGTGCGCACGAGTGAGGACAAAGTGTGCAGAAAAGACACG

Reverse complement sequence

CGTGTCTTTTCTGCACACTTTGTCCTCACTCGTGCGCACCGGAAAGACGTCCCCGTCGATTAACCCCAGGCCAGGAACGTCCCCTCTTCGCCACGTCCCC[C/T]
GTCGATTAACCCCAGGCCACCTCACTCGTGCGCACCAGGAAGTGGCCCTCTTGGCCACGTCCGCCACCTCACTCGTGCGCACCGGGAAGACGTCCCCGTC

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 84.00% 4.30% 9.71% 1.99% NA
All Indica  2759 90.70% 2.20% 3.91% 3.19% NA
All Japonica  1512 72.90% 7.90% 19.05% 0.07% NA
Aus  269 98.50% 0.00% 0.37% 1.12% NA
Indica I  595 91.40% 0.00% 6.72% 1.85% NA
Indica II  465 91.40% 0.40% 4.73% 3.44% NA
Indica III  913 88.20% 5.90% 2.74% 3.18% NA
Indica Intermediate  786 92.70% 0.50% 2.67% 4.07% NA
Temperate Japonica  767 98.00% 0.70% 1.30% 0.00% NA
Tropical Japonica  504 40.30% 18.50% 41.07% 0.20% NA
Japonica Intermediate  241 61.40% 9.10% 29.46% 0.00% NA
VI/Aromatic  96 33.30% 19.80% 45.83% 1.04% NA
Intermediate  90 76.70% 2.20% 20.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0810597423 G -> A LOC_Os08g17320.1 downstream_gene_variant ; 4095.0bp to feature; MODIFIER silent_mutation Average:80.9; most accessible tissue: Minghui63 panicle, score: 91.034 N N N N
vg0810597423 G -> A LOC_Os08g17320-LOC_Os08g17330 intergenic_region ; MODIFIER silent_mutation Average:80.9; most accessible tissue: Minghui63 panicle, score: 91.034 N N N N
vg0810597423 G -> DEL N N silent_mutation Average:80.9; most accessible tissue: Minghui63 panicle, score: 91.034 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)
vg0810597423 G A -0.02 0.0 0.0 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0810597423 NA 4.74E-15 mr1084 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
vg0810597423 NA 1.22E-15 mr1205 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
vg0810597423 2.46E-06 2.15E-11 mr1206 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
vg0810597423 NA 7.01E-09 mr1206 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
vg0810597423 NA 2.24E-07 mr1229 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
vg0810597423 NA 3.37E-07 mr1229 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
vg0810597423 NA 8.56E-16 mr1330 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
vg0810597423 NA 1.15E-11 mr1332 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
vg0810597423 NA 3.39E-07 mr1338 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
vg0810597423 NA 3.59E-14 mr1454 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
vg0810597423 NA 2.47E-13 mr1521 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
vg0810597423 NA 3.95E-08 mr1570 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
vg0810597423 NA 4.67E-08 mr1596 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
vg0810597423 NA 9.07E-09 mr1668 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
vg0810597423 NA 4.17E-07 mr1668 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
vg0810597423 NA 9.74E-06 mr1763 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
vg0810597423 NA 9.56E-13 mr1775 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
vg0810597423 NA 5.70E-07 mr1851 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
vg0810597423 NA 7.24E-12 mr1864 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
vg0810597423 NA 1.79E-06 mr1880 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