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Detailed information for vg0724265685:

Variant ID: vg0724265685 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 24265685
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.65, C: 0.35, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


GTGAGAATCGTGGGGGCAAGTATGGGAGCGCGAAACGAGGAGGCGAGCGCGGATGAGGCGAGGATAAAAGGGGGCGGAGGCGGAGACTCTGCCCCCTTCC[C/T]
TTCGCCAACCGCCCACTCGTCCTTTCGCTTCTCGAACCCTAACATTCTCGCCACCCCATTCCGTCTCGCGCCCCATGCTCTCCGCCACCTCTCCGCCGGT

Reverse complement sequence

ACCGGCGGAGAGGTGGCGGAGAGCATGGGGCGCGAGACGGAATGGGGTGGCGAGAATGTTAGGGTTCGAGAAGCGAAAGGACGAGTGGGCGGTTGGCGAA[G/A]
GGAAGGGGGCAGAGTCTCCGCCTCCGCCCCCTTTTATCCTCGCCTCATCCGCGCTCGCCTCCTCGTTTCGCGCTCCCATACTTGCCCCCACGATTCTCAC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.30% 38.70% 0.70% 0.32% NA
All Indica  2759 95.40% 4.10% 0.14% 0.36% NA
All Japonica  1512 2.60% 97.20% 0.00% 0.13% NA
Aus  269 25.30% 67.70% 7.06% 0.00% NA
Indica I  595 99.20% 0.70% 0.00% 0.17% NA
Indica II  465 88.20% 11.00% 0.22% 0.65% NA
Indica III  913 97.40% 2.30% 0.00% 0.33% NA
Indica Intermediate  786 94.40% 4.80% 0.38% 0.38% NA
Temperate Japonica  767 0.80% 99.20% 0.00% 0.00% NA
Tropical Japonica  504 2.20% 97.80% 0.00% 0.00% NA
Japonica Intermediate  241 9.50% 89.60% 0.00% 0.83% NA
VI/Aromatic  96 72.90% 22.90% 4.17% 0.00% NA
Intermediate  90 44.40% 45.60% 6.67% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0724265685 C -> DEL N N silent_mutation Average:79.473; most accessible tissue: Minghui63 root, score: 88.175 N N N N
vg0724265685 C -> T LOC_Os07g40490.1 downstream_gene_variant ; 4275.0bp to feature; MODIFIER silent_mutation Average:79.473; most accessible tissue: Minghui63 root, score: 88.175 N N N N
vg0724265685 C -> T LOC_Os07g40510.1 downstream_gene_variant ; 791.0bp to feature; MODIFIER silent_mutation Average:79.473; most accessible tissue: Minghui63 root, score: 88.175 N N N N
vg0724265685 C -> T LOC_Os07g40490-LOC_Os07g40510 intergenic_region ; MODIFIER silent_mutation Average:79.473; most accessible tissue: Minghui63 root, score: 88.175 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)
vg0724265685 C T -0.03 -0.03 -0.03 -0.02 -0.03 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0724265685 NA 1.07E-07 mr1082 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
vg0724265685 NA 5.24E-06 mr1103 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
vg0724265685 NA 4.45E-11 mr1172 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
vg0724265685 NA 9.00E-09 mr1249 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
vg0724265685 NA 1.28E-34 mr1404 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
vg0724265685 NA 7.31E-06 mr1782 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
vg0724265685 NA 5.13E-34 mr1878 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
vg0724265685 NA 2.14E-06 mr1990 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
vg0724265685 7.29E-07 7.29E-07 mr1067_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
vg0724265685 NA 4.83E-06 mr1071_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
vg0724265685 NA 2.61E-32 mr1083_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
vg0724265685 NA 3.67E-38 mr1104_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
vg0724265685 NA 3.46E-07 mr1203_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
vg0724265685 NA 2.35E-06 mr1402_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
vg0724265685 NA 6.73E-53 mr1404_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
vg0724265685 1.01E-06 4.68E-07 mr1404_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
vg0724265685 NA 9.91E-06 mr1613_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
vg0724265685 NA 2.65E-48 mr1620_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
vg0724265685 NA 1.07E-35 mr1878_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