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Detailed information for vg0312684585:

Variant ID: vg0312684585 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 12684585
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCGAAATATCTGGATGGATGGGTTCTCAAATAAAGCCCAAATAAATACGGTAACCATCCAACCTCATCGCAGGCCCCGACATGTCTTGAAGAGTGCACT[A/G]
CATAGGCTCTAAGCCATCGGATATGAAATAGAAGACACAACTGTTGGAATAGCCACACCAATCATCTACGTCATACGCCCGTCAACCACTCGATGGTGGC

Reverse complement sequence

GCCACCATCGAGTGGTTGACGGGCGTATGACGTAGATGATTGGTGTGGCTATTCCAACAGTTGTGTCTTCTATTTCATATCCGATGGCTTAGAGCCTATG[T/C]
AGTGCACTCTTCAAGACATGTCGGGGCCTGCGATGAGGTTGGATGGTTACCGTATTTATTTGGGCTTTATTTGAGAACCCATCCATCCAGATATTTCGCG

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 96.60% 2.80% 0.59% 0.00% NA
All Indica  2759 99.50% 0.00% 0.47% 0.00% NA
All Japonica  1512 90.70% 8.40% 0.93% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.30% 0.00% 1.68% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.00% 0.38% 0.00% NA
Temperate Japonica  767 99.60% 0.30% 0.13% 0.00% NA
Tropical Japonica  504 75.20% 22.80% 1.98% 0.00% NA
Japonica Intermediate  241 94.60% 4.10% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 6.70% 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
vg0312684585 A -> G LOC_Os03g22120.1 upstream_gene_variant ; 3928.0bp to feature; MODIFIER silent_mutation Average:52.979; most accessible tissue: Minghui63 young leaf, score: 82.642 N N N N
vg0312684585 A -> G LOC_Os03g22130.1 upstream_gene_variant ; 2640.0bp to feature; MODIFIER silent_mutation Average:52.979; most accessible tissue: Minghui63 young leaf, score: 82.642 N N N N
vg0312684585 A -> G LOC_Os03g22120.3 upstream_gene_variant ; 4422.0bp to feature; MODIFIER silent_mutation Average:52.979; most accessible tissue: Minghui63 young leaf, score: 82.642 N N N N
vg0312684585 A -> G LOC_Os03g22120.2 upstream_gene_variant ; 3928.0bp to feature; MODIFIER silent_mutation Average:52.979; most accessible tissue: Minghui63 young leaf, score: 82.642 N N N N
vg0312684585 A -> G LOC_Os03g22120-LOC_Os03g22130 intergenic_region ; MODIFIER silent_mutation Average:52.979; most accessible tissue: Minghui63 young leaf, score: 82.642 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)
vg0312684585 A G 0.02 0.0 0.01 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0312684585 1.55E-07 NA mr1076 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
vg0312684585 2.27E-06 NA mr1083 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
vg0312684585 2.80E-06 2.80E-06 mr1085 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
vg0312684585 NA 3.17E-06 mr1088 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
vg0312684585 NA 8.12E-07 mr1104 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
vg0312684585 NA 6.99E-06 mr1139 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
vg0312684585 NA 4.72E-07 mr1155 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
vg0312684585 NA 7.57E-07 mr1213 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
vg0312684585 5.36E-08 NA mr1226 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
vg0312684585 NA 8.22E-06 mr1277 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
vg0312684585 3.99E-07 2.25E-06 mr1411 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
vg0312684585 2.67E-06 1.10E-07 mr1437 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
vg0312684585 NA 1.99E-07 mr1620 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
vg0312684585 NA 1.06E-06 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
vg0312684585 NA 9.64E-07 mr1951 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
vg0312684585 4.02E-06 NA mr1104_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
vg0312684585 3.53E-06 2.32E-06 mr1155_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
vg0312684585 8.34E-06 NA mr1226_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
vg0312684585 NA 3.73E-06 mr1558_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