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Detailed information for vg0613566824:

Variant ID: vg0613566824 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 13566824
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


GCAACATCTTCAAAATGCGAATTTGTGTTTTTGAAAAAAAACAAAAATCACAAAGTGAAAAGGAAAACTCTCCCTTTTTAAAAGAGAGTTACAGTGTGCC[C/A]
TGCCTAATAGGATCTGCTTGCTATTTAAAGCGAAAAAGGTGTCCCTGCCAGAACCGACTCGTTACGGTGTGCAAAATCCGACTCGACGCAGTGTGCGAAA

Reverse complement sequence

TTTCGCACACTGCGTCGAGTCGGATTTTGCACACCGTAACGAGTCGGTTCTGGCAGGGACACCTTTTTCGCTTTAAATAGCAAGCAGATCCTATTAGGCA[G/T]
GGCACACTGTAACTCTCTTTTAAAAAGGGAGAGTTTTCCTTTTCACTTTGTGATTTTTGTTTTTTTTCAAAAACACAAATTCGCATTTTGAAGATGTTGC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.20% 39.50% 0.02% 0.32% NA
All Indica  2759 94.90% 4.70% 0.04% 0.40% NA
All Japonica  1512 2.20% 97.60% 0.00% 0.13% NA
Aus  269 52.00% 48.00% 0.00% 0.00% NA
Indica I  595 93.10% 6.60% 0.00% 0.34% NA
Indica II  465 96.10% 3.20% 0.00% 0.65% NA
Indica III  913 97.40% 2.20% 0.11% 0.33% NA
Indica Intermediate  786 92.60% 7.00% 0.00% 0.38% NA
Temperate Japonica  767 3.40% 96.30% 0.00% 0.26% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 13.50% 86.50% 0.00% 0.00% NA
Intermediate  90 44.40% 53.30% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0613566824 C -> A LOC_Os06g23230.1 upstream_gene_variant ; 323.0bp to feature; MODIFIER silent_mutation Average:69.228; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N
vg0613566824 C -> A LOC_Os06g23240.1 upstream_gene_variant ; 1241.0bp to feature; MODIFIER silent_mutation Average:69.228; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N
vg0613566824 C -> A LOC_Os06g23230-LOC_Os06g23240 intergenic_region ; MODIFIER silent_mutation Average:69.228; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N
vg0613566824 C -> DEL N N silent_mutation Average:69.228; most accessible tissue: Minghui63 panicle, score: 82.797 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)
vg0613566824 C A -0.05 -0.04 -0.04 -0.06 -0.05 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0613566824 NA 1.72E-21 mr1020 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
vg0613566824 3.45E-06 2.24E-12 mr1033 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
vg0613566824 NA 3.28E-40 mr1064 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
vg0613566824 NA 1.02E-43 mr1067 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
vg0613566824 NA 5.53E-07 mr1176 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
vg0613566824 NA 1.14E-29 mr1204 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
vg0613566824 NA 1.31E-12 mr1301 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
vg0613566824 1.30E-06 4.98E-13 mr1410 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
vg0613566824 NA 1.77E-44 mr1534 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
vg0613566824 NA 8.26E-06 mr1993 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
vg0613566824 NA 3.06E-19 mr1033_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
vg0613566824 NA 5.99E-56 mr1067_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
vg0613566824 NA 8.15E-09 mr1548_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
vg0613566824 NA 3.83E-15 mr1744_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
vg0613566824 NA 4.48E-14 mr1938_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
vg0613566824 NA 9.07E-10 mr1993_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