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Detailed information for vg0217338921:

Variant ID: vg0217338921 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 17338921
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCCCAGGGAGTCAAATTGCACTGGTTTTAAGAGTTTGGGGGTCGAGATGTCCGGTTTTGTGGTTTAGGGTCATGGATTAGATTTCGATCACTTTTGAGG[G/A]
TCATGAAGTGAACTTATTCCAAAGGGCTTGCTATCCCTCCCACAATCTTCCTCCTTTTCAGGCCCATTGGCCCAATAAAAAAAAAGCGCCCAAACACTAT

Reverse complement sequence

ATAGTGTTTGGGCGCTTTTTTTTTATTGGGCCAATGGGCCTGAAAAGGAGGAAGATTGTGGGAGGGATAGCAAGCCCTTTGGAATAAGTTCACTTCATGA[C/T]
CCTCAAAAGTGATCGAAATCTAATCCATGACCCTAAACCACAAAACCGGACATCTCGACCCCCAAACTCTTAAAACCAGTGCAATTTGACTCCCTGGGCG

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 87.80% 11.00% 1.16% 0.00% NA
All Indica  2759 79.40% 18.70% 1.92% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.00% 2.50% 0.50% 0.00% NA
Indica II  465 92.90% 5.80% 1.29% 0.00% NA
Indica III  913 57.80% 39.00% 3.18% 0.00% NA
Indica Intermediate  786 83.10% 15.00% 1.91% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 95.60% 3.30% 1.11% 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
vg0217338921 G -> A LOC_Os02g29210.1 upstream_gene_variant ; 3307.0bp to feature; MODIFIER silent_mutation Average:95.925; most accessible tissue: Minghui63 panicle, score: 99.785 N N N N
vg0217338921 G -> A LOC_Os02g29210.3 upstream_gene_variant ; 3328.0bp to feature; MODIFIER silent_mutation Average:95.925; most accessible tissue: Minghui63 panicle, score: 99.785 N N N N
vg0217338921 G -> A LOC_Os02g29210.2 upstream_gene_variant ; 3307.0bp to feature; MODIFIER silent_mutation Average:95.925; most accessible tissue: Minghui63 panicle, score: 99.785 N N N N
vg0217338921 G -> A LOC_Os02g29210.4 upstream_gene_variant ; 3307.0bp to feature; MODIFIER silent_mutation Average:95.925; most accessible tissue: Minghui63 panicle, score: 99.785 N N N N
vg0217338921 G -> A LOC_Os02g29220.1 intron_variant ; MODIFIER silent_mutation Average:95.925; most accessible tissue: Minghui63 panicle, score: 99.785 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)
vg0217338921 G A -0.35 -0.35 -0.28 -0.25 -0.26 -0.27

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0217338921 1.08E-06 NA mr1109 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
vg0217338921 2.64E-08 NA mr1129 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
vg0217338921 1.02E-07 1.65E-06 mr1129 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
vg0217338921 5.43E-06 NA mr1251 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
vg0217338921 4.41E-06 NA mr1257 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
vg0217338921 NA 7.19E-06 mr1423 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
vg0217338921 5.62E-06 NA mr1089_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
vg0217338921 3.32E-06 NA mr1109_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
vg0217338921 1.32E-06 NA mr1129_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
vg0217338921 1.44E-06 NA mr1129_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
vg0217338921 4.67E-06 NA mr1251_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
vg0217338921 6.97E-06 NA mr1253_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
vg0217338921 NA 9.15E-06 mr1253_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
vg0217338921 2.00E-08 NA mr1255_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
vg0217338921 1.59E-07 5.46E-07 mr1255_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
vg0217338921 7.13E-07 NA mr1257_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
vg0217338921 1.64E-06 NA mr1257_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
vg0217338921 5.50E-06 NA mr1435_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