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Detailed information for vg0217524100:

Variant ID: vg0217524100 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 17524100
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


CTGAAAAATCGAGCCGTGACAAGTCTCATGTGCTGGGTGCGTCACGGAGTGTGGGATTAAAAGCGTACATCCACTGCAGTGTGAGTAAACCAATCTATTC[G/A]
AATAGCCGTGCTCGCGGCTAATACCCTTGACTAGACTCATAGATTTTGATCCTACTTAGAGTAAATATAAGAGACATGTGAACCTTGCCCAAAGAGTGGG

Reverse complement sequence

CCCACTCTTTGGGCAAGGTTCACATGTCTCTTATATTTACTCTAAGTAGGATCAAAATCTATGAGTCTAGTCAAGGGTATTAGCCGCGAGCACGGCTATT[C/T]
GAATAGATTGGTTTACTCACACTGCAGTGGATGTACGCTTTTAATCCCACACTCCGTGACGCACCCAGCACATGAGACTTGTCACGGCTCGATTTTTCAG

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 61.50% 24.20% 0.59% 13.69% NA
All Indica  2759 43.30% 32.90% 1.01% 22.76% NA
All Japonica  1512 97.90% 1.50% 0.00% 0.60% NA
Aus  269 60.20% 39.80% 0.00% 0.00% NA
Indica I  595 28.40% 36.80% 1.68% 33.11% NA
Indica II  465 47.30% 11.00% 1.94% 39.78% NA
Indica III  913 58.10% 41.50% 0.00% 0.44% NA
Indica Intermediate  786 35.20% 32.80% 1.15% 30.79% NA
Temperate Japonica  767 98.70% 0.40% 0.00% 0.91% NA
Tropical Japonica  504 97.00% 2.80% 0.00% 0.20% NA
Japonica Intermediate  241 97.10% 2.50% 0.00% 0.41% NA
VI/Aromatic  96 9.40% 90.60% 0.00% 0.00% NA
Intermediate  90 64.40% 24.40% 0.00% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0217524100 G -> A LOC_Os02g29500.1 upstream_gene_variant ; 2447.0bp to feature; MODIFIER silent_mutation Average:76.032; most accessible tissue: Minghui63 flag leaf, score: 88.687 N N N N
vg0217524100 G -> A LOC_Os02g29510.2 upstream_gene_variant ; 4515.0bp to feature; MODIFIER silent_mutation Average:76.032; most accessible tissue: Minghui63 flag leaf, score: 88.687 N N N N
vg0217524100 G -> A LOC_Os02g29510.3 upstream_gene_variant ; 3450.0bp to feature; MODIFIER silent_mutation Average:76.032; most accessible tissue: Minghui63 flag leaf, score: 88.687 N N N N
vg0217524100 G -> A LOC_Os02g29490.1 downstream_gene_variant ; 4470.0bp to feature; MODIFIER silent_mutation Average:76.032; most accessible tissue: Minghui63 flag leaf, score: 88.687 N N N N
vg0217524100 G -> A LOC_Os02g29500-LOC_Os02g29510 intergenic_region ; MODIFIER silent_mutation Average:76.032; most accessible tissue: Minghui63 flag leaf, score: 88.687 N N N N
vg0217524100 G -> DEL N N silent_mutation Average:76.032; most accessible tissue: Minghui63 flag leaf, score: 88.687 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)
vg0217524100 G A -0.01 -0.01 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0217524100 NA 6.23E-06 mr1236 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
vg0217524100 6.67E-07 NA mr1927 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
vg0217524100 9.40E-06 2.66E-06 mr1927 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
vg0217524100 4.02E-06 4.85E-07 mr1236_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
vg0217524100 5.60E-06 6.31E-09 mr1236_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
vg0217524100 5.45E-09 3.28E-10 mr1317_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
vg0217524100 6.93E-07 7.86E-07 mr1317_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
vg0217524100 4.31E-07 NA mr1610_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
vg0217524100 6.65E-06 NA mr1610_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
vg0217524100 3.67E-08 NA mr1818_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
vg0217524100 1.99E-08 NA mr1855_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
vg0217524100 2.81E-06 NA mr1855_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
vg0217524100 NA 3.17E-06 mr1880_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
vg0217524100 8.13E-09 NA mr1897_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
vg0217524100 8.18E-07 2.16E-06 mr1897_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
vg0217524100 1.39E-08 NA mr1914_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
vg0217524100 3.08E-06 4.87E-06 mr1914_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
vg0217524100 2.47E-09 NA mr1927_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
vg0217524100 4.44E-06 3.89E-06 mr1927_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