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Detailed information for vg0629150340:

Variant ID: vg0629150340 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 29150340
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCACAGGCCTTCCCGTTGTCAATGCGGACGATTTGTGGTCTCACCGGCTATCGAATCGCAGTAGCAAGATGTGGATGCATCCGGTAAGTACTATAAGTCT[A/G]
TAACTCCTATTACCAATATTGATCGGGGATTTTTTTTTTCGCGAACAGATAAAATGATTACACGTCAATATATTATAAGAAAACGAGTTTTTGTTACACA

Reverse complement sequence

TGTGTAACAAAAACTCGTTTTCTTATAATATATTGACGTGTAATCATTTTATCTGTTCGCGAAAAAAAAAATCCCCGATCAATATTGGTAATAGGAGTTA[T/C]
AGACTTATAGTACTTACCGGATGCATCCACATCTTGCTACTGCGATTCGATAGCCGGTGAGACCACAAATCGTCCGCATTGACAACGGGAAGGCCTGTGA

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 75.50% 6.70% 8.04% 9.75% NA
All Indica  2759 74.50% 0.60% 9.71% 15.22% NA
All Japonica  1512 78.60% 18.70% 1.59% 1.12% NA
Aus  269 76.20% 0.40% 20.07% 3.35% NA
Indica I  595 59.00% 0.00% 15.63% 25.38% NA
Indica II  465 71.00% 0.60% 10.32% 18.06% NA
Indica III  913 86.70% 0.10% 4.71% 8.43% NA
Indica Intermediate  786 74.00% 1.50% 10.69% 13.74% NA
Temperate Japonica  767 96.50% 1.70% 0.26% 1.56% NA
Tropical Japonica  504 48.20% 48.00% 3.37% 0.40% NA
Japonica Intermediate  241 85.50% 11.20% 2.07% 1.24% NA
VI/Aromatic  96 70.80% 4.20% 21.88% 3.12% NA
Intermediate  90 58.90% 13.30% 14.44% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0629150340 A -> G LOC_Os06g48180.1 downstream_gene_variant ; 3778.0bp to feature; MODIFIER silent_mutation Average:81.796; most accessible tissue: Minghui63 panicle, score: 96.546 N N N N
vg0629150340 A -> G LOC_Os06g48190.1 downstream_gene_variant ; 1718.0bp to feature; MODIFIER silent_mutation Average:81.796; most accessible tissue: Minghui63 panicle, score: 96.546 N N N N
vg0629150340 A -> G LOC_Os06g48180.2 downstream_gene_variant ; 3778.0bp to feature; MODIFIER silent_mutation Average:81.796; most accessible tissue: Minghui63 panicle, score: 96.546 N N N N
vg0629150340 A -> G LOC_Os06g48190-LOC_Os06g48200 intergenic_region ; MODIFIER silent_mutation Average:81.796; most accessible tissue: Minghui63 panicle, score: 96.546 N N N N
vg0629150340 A -> DEL N N silent_mutation Average:81.796; most accessible tissue: Minghui63 panicle, score: 96.546 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)
vg0629150340 A G 0.04 -0.05 -0.02 0.03 0.02 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0629150340 4.49E-06 NA mr1188 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
vg0629150340 NA 8.52E-06 mr1502 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
vg0629150340 NA 2.31E-06 mr1502 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
vg0629150340 NA 7.85E-07 mr1543 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
vg0629150340 NA 1.00E-07 mr1543 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
vg0629150340 9.60E-06 1.32E-31 mr1699 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
vg0629150340 NA 2.03E-17 mr1699 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
vg0629150340 1.26E-11 1.86E-21 mr1871 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
vg0629150340 1.02E-07 1.98E-11 mr1871 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
vg0629150340 9.03E-07 NA mr1188_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
vg0629150340 NA 2.54E-08 mr1449_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
vg0629150340 NA 1.71E-06 mr1449_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
vg0629150340 NA 6.14E-09 mr1543_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
vg0629150340 NA 3.57E-07 mr1696_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
vg0629150340 7.10E-08 1.38E-16 mr1742_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
vg0629150340 3.24E-06 5.62E-10 mr1742_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
vg0629150340 9.78E-11 1.63E-24 mr1871_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
vg0629150340 2.07E-06 1.54E-09 mr1871_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
vg0629150340 NA 3.12E-06 mr1966_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