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Detailed information for vg1002842933:

Variant ID: vg1002842933 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2842933
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTTCAAAGGAGCTATCTGACAGTTCCAGTATTTCCTGTTGTAGAGAGAACCAACGGGACTTAAACTGCAAAGAAGTCCTACACGAATCATCAATCAATA[G/A]
CTCCCCTAACCCCACCGTTTCTCTCATTTTTTTGGATTATTTTTGGGCTCCTTGTTTAATTTACACGTTGTCTTTTACTGTTTTGGGCTCCTCATGCAGA

Reverse complement sequence

TCTGCATGAGGAGCCCAAAACAGTAAAAGACAACGTGTAAATTAAACAAGGAGCCCAAAAATAATCCAAAAAAATGAGAGAAACGGTGGGGTTAGGGGAG[C/T]
TATTGATTGATGATTCGTGTAGGACTTCTTTGCAGTTTAAGTCCCGTTGGTTCTCTCTACAACAGGAAATACTGGAACTGTCAGATAGCTCCTTTGAACA

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 54.00% 19.90% 6.01% 20.06% NA
All Indica  2759 85.60% 3.00% 6.42% 4.97% NA
All Japonica  1512 2.20% 54.70% 2.31% 40.81% NA
Aus  269 12.30% 1.50% 21.93% 64.31% NA
Indica I  595 98.00% 0.20% 0.34% 1.51% NA
Indica II  465 69.70% 1.30% 16.99% 12.04% NA
Indica III  913 84.80% 7.00% 5.59% 2.63% NA
Indica Intermediate  786 86.80% 1.40% 5.73% 6.11% NA
Temperate Japonica  767 0.70% 83.80% 2.74% 12.78% NA
Tropical Japonica  504 4.00% 8.50% 0.79% 86.71% NA
Japonica Intermediate  241 3.30% 58.50% 4.15% 34.02% NA
VI/Aromatic  96 86.50% 9.40% 4.17% 0.00% NA
Intermediate  90 44.40% 22.20% 10.00% 23.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1002842933 G -> A LOC_Os10g05680.1 upstream_gene_variant ; 361.0bp to feature; MODIFIER silent_mutation Average:85.049; most accessible tissue: Callus, score: 96.142 N N N N
vg1002842933 G -> A LOC_Os10g05680.2 upstream_gene_variant ; 361.0bp to feature; MODIFIER silent_mutation Average:85.049; most accessible tissue: Callus, score: 96.142 N N N N
vg1002842933 G -> A LOC_Os10g05660-LOC_Os10g05680 intergenic_region ; MODIFIER silent_mutation Average:85.049; most accessible tissue: Callus, score: 96.142 N N N N
vg1002842933 G -> DEL N N silent_mutation Average:85.049; most accessible tissue: Callus, score: 96.142 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)
vg1002842933 G A -0.02 0.0 -0.01 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002842933 NA 4.77E-15 mr1164 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
vg1002842933 2.27E-06 4.57E-16 mr1933 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
vg1002842933 NA 8.30E-10 mr1945 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
vg1002842933 NA 1.10E-10 mr1050_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
vg1002842933 NA 3.29E-08 mr1084_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
vg1002842933 NA 3.68E-10 mr1198_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
vg1002842933 NA 5.77E-08 mr1205_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
vg1002842933 NA 3.51E-13 mr1217_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
vg1002842933 NA 1.18E-06 mr1227_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
vg1002842933 NA 6.55E-11 mr1228_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
vg1002842933 NA 1.63E-07 mr1272_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
vg1002842933 NA 4.97E-07 mr1275_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
vg1002842933 NA 2.06E-21 mr1298_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
vg1002842933 NA 6.85E-06 mr1407_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
vg1002842933 NA 2.65E-07 mr1446_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
vg1002842933 NA 8.67E-15 mr1575_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
vg1002842933 NA 1.97E-07 mr1607_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
vg1002842933 4.89E-06 NA mr1711_2 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
vg1002842933 NA 7.41E-22 mr1731_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
vg1002842933 NA 5.43E-06 mr1869_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
vg1002842933 NA 8.83E-08 mr1909_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
vg1002842933 NA 8.69E-09 mr1940_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