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Detailed information for vg0231913229:

Variant ID: vg0231913229 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 31913229
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTATGATATGTTGATGTGATGAAAAAGGACTGAAATTTGGATCCAAACTTTGAATCTAAACACAGCCCTGATGAGATCCAAGGCCCTCACCATTGGACG[A/G]
TGCAGGGCTACAGGAAATGGTGGGAGCCCGGATCGGACGGCGACGAGACAGCGTCGTGCTTTACGGGCTGGTACTGGCCGTCTGGCCGTGGCCGGTGATG

Reverse complement sequence

CATCACCGGCCACGGCCAGACGGCCAGTACCAGCCCGTAAAGCACGACGCTGTCTCGTCGCCGTCCGATCCGGGCTCCCACCATTTCCTGTAGCCCTGCA[T/C]
CGTCCAATGGTGAGGGCCTTGGATCTCATCAGGGCTGTGTTTAGATTCAAAGTTTGGATCCAAATTTCAGTCCTTTTTCATCACATCAACATATCATACA

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 83.30% 16.10% 0.59% 0.00% NA
All Indica  2759 99.60% 0.40% 0.04% 0.00% NA
All Japonica  1512 49.80% 48.50% 1.72% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.00% 0.90% 0.13% 0.00% NA
Temperate Japonica  767 13.80% 84.10% 2.09% 0.00% NA
Tropical Japonica  504 94.40% 4.80% 0.79% 0.00% NA
Japonica Intermediate  241 71.00% 26.60% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 82.20% 16.70% 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
vg0231913229 A -> G LOC_Os02g52130.1 downstream_gene_variant ; 1532.0bp to feature; MODIFIER silent_mutation Average:91.486; most accessible tissue: Callus, score: 99.127 N N N N
vg0231913229 A -> G LOC_Os02g52140.1 downstream_gene_variant ; 2878.0bp to feature; MODIFIER silent_mutation Average:91.486; most accessible tissue: Callus, score: 99.127 N N N N
vg0231913229 A -> G LOC_Os02g52130.2 downstream_gene_variant ; 1577.0bp to feature; MODIFIER silent_mutation Average:91.486; most accessible tissue: Callus, score: 99.127 N N N N
vg0231913229 A -> G LOC_Os02g52130.3 downstream_gene_variant ; 1577.0bp to feature; MODIFIER silent_mutation Average:91.486; most accessible tissue: Callus, score: 99.127 N N N N
vg0231913229 A -> G LOC_Os02g52130.4 downstream_gene_variant ; 1577.0bp to feature; MODIFIER silent_mutation Average:91.486; most accessible tissue: Callus, score: 99.127 N N N N
vg0231913229 A -> G LOC_Os02g52130.5 downstream_gene_variant ; 1577.0bp to feature; MODIFIER silent_mutation Average:91.486; most accessible tissue: Callus, score: 99.127 N N N N
vg0231913229 A -> G LOC_Os02g52130.6 downstream_gene_variant ; 1577.0bp to feature; MODIFIER silent_mutation Average:91.486; most accessible tissue: Callus, score: 99.127 N N N N
vg0231913229 A -> G LOC_Os02g52130.7 downstream_gene_variant ; 1577.0bp to feature; MODIFIER silent_mutation Average:91.486; most accessible tissue: Callus, score: 99.127 N N N N
vg0231913229 A -> G LOC_Os02g52130.8 downstream_gene_variant ; 1577.0bp to feature; MODIFIER silent_mutation Average:91.486; most accessible tissue: Callus, score: 99.127 N N N N
vg0231913229 A -> G LOC_Os02g52130.9 downstream_gene_variant ; 1577.0bp to feature; MODIFIER silent_mutation Average:91.486; most accessible tissue: Callus, score: 99.127 N N N N
vg0231913229 A -> G LOC_Os02g52140.2 downstream_gene_variant ; 2878.0bp to feature; MODIFIER silent_mutation Average:91.486; most accessible tissue: Callus, score: 99.127 N N N N
vg0231913229 A -> G LOC_Os02g52130-LOC_Os02g52140 intergenic_region ; MODIFIER silent_mutation Average:91.486; most accessible tissue: Callus, score: 99.127 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)
vg0231913229 A G 0.07 0.06 0.09 0.13 0.07 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0231913229 NA 8.60E-14 Grain_length All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0231913229 NA 9.44E-14 Grain_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0231913229 NA 6.04E-07 mr1163 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
vg0231913229 NA 4.20E-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
vg0231913229 NA 1.13E-06 mr1570 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
vg0231913229 NA 1.78E-10 mr1712 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
vg0231913229 NA 2.04E-06 mr1977 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
vg0231913229 NA 2.83E-20 mr1010_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
vg0231913229 NA 1.26E-11 mr1087_2 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
vg0231913229 NA 2.07E-06 mr1206_2 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
vg0231913229 NA 3.10E-07 mr1229_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
vg0231913229 NA 9.84E-08 mr1229_2 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
vg0231913229 NA 6.36E-08 mr1338_2 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
vg0231913229 NA 3.43E-09 mr1486_2 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
vg0231913229 NA 4.23E-09 mr1543_2 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
vg0231913229 NA 1.29E-09 mr1570_2 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
vg0231913229 NA 2.24E-10 mr1580_2 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
vg0231913229 NA 3.17E-07 mr1763_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
vg0231913229 NA 5.33E-11 mr1789_2 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
vg0231913229 NA 1.03E-09 mr1825_2 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
vg0231913229 NA 1.02E-11 mr1844_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
vg0231913229 NA 9.44E-06 mr1844_2 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
vg0231913229 3.91E-06 1.78E-08 mr1865_2 Jap_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
vg0231913229 NA 2.17E-07 mr1880_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
vg0231913229 NA 1.13E-07 mr1880_2 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
vg0231913229 NA 1.16E-06 mr1977_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