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Detailed information for vg0624805039:

Variant ID: vg0624805039 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 24805039
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:


AAGATACGCAAAACGAGGTGAGCTATTAGCTCATGATTAATTGAGTATTAACTATTTTAAATTTCAAAAATAAATTAATATGATTTTTTAAAGCAACTTT[C/T]
CTATAGAAAATTTTTACAAAAAACACAAGTTTGGAAAACATACATAAGAAAAACGAATCAAACAAACTCACCCTCTCACCCTCTCGAACGCTGCTAAGCG

Reverse complement sequence

CGCTTAGCAGCGTTCGAGAGGGTGAGAGGGTGAGTTTGTTTGATTCGTTTTTCTTATGTATGTTTTCCAAACTTGTGTTTTTTGTAAAAATTTTCTATAG[G/A]
AAAGTTGCTTTAAAAAATCATATTAATTTATTTTTGAAATTTAAAATAGTTAATACTCAATTAATCATGAGCTAATAGCTCACCTCGTTTTGCGTATCTT

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 57.40% 35.60% 2.58% 4.34% NA
All Indica  2759 84.90% 3.80% 4.17% 7.14% NA
All Japonica  1512 5.30% 94.40% 0.33% 0.00% NA
Aus  269 88.80% 9.70% 0.00% 1.49% NA
Indica I  595 84.50% 0.00% 5.71% 9.75% NA
Indica II  465 76.80% 5.40% 7.96% 9.89% NA
Indica III  913 93.30% 1.40% 1.75% 3.50% NA
Indica Intermediate  786 80.30% 8.40% 3.56% 7.76% NA
Temperate Japonica  767 1.20% 98.20% 0.65% 0.00% NA
Tropical Japonica  504 13.50% 86.50% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 16.70% 83.30% 0.00% 0.00% NA
Intermediate  90 41.10% 52.20% 2.22% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0624805039 C -> T LOC_Os06g41380.1 upstream_gene_variant ; 507.0bp to feature; MODIFIER silent_mutation Average:98.946; most accessible tissue: Zhenshan97 flag leaf, score: 99.411 N N N N
vg0624805039 C -> T LOC_Os06g41384.1 downstream_gene_variant ; 3718.0bp to feature; MODIFIER silent_mutation Average:98.946; most accessible tissue: Zhenshan97 flag leaf, score: 99.411 N N N N
vg0624805039 C -> T LOC_Os06g41384.2 downstream_gene_variant ; 3718.0bp to feature; MODIFIER silent_mutation Average:98.946; most accessible tissue: Zhenshan97 flag leaf, score: 99.411 N N N N
vg0624805039 C -> T LOC_Os06g41370-LOC_Os06g41380 intergenic_region ; MODIFIER silent_mutation Average:98.946; most accessible tissue: Zhenshan97 flag leaf, score: 99.411 N N N N
vg0624805039 C -> DEL N N silent_mutation Average:98.946; most accessible tissue: Zhenshan97 flag leaf, score: 99.411 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)
vg0624805039 C T -0.01 0.0 0.0 -0.01 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0624805039 NA 1.63E-06 mr1028 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
vg0624805039 NA 2.96E-06 mr1092 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
vg0624805039 NA 2.39E-40 mr1124 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
vg0624805039 NA 4.51E-07 mr1154 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
vg0624805039 NA 3.28E-08 mr1190 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
vg0624805039 NA 2.83E-08 mr1245 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
vg0624805039 6.26E-06 1.68E-06 mr1245 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
vg0624805039 NA 3.21E-22 mr1254 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
vg0624805039 NA 3.51E-30 mr1256 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
vg0624805039 NA 3.52E-16 mr1276 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
vg0624805039 3.26E-06 7.97E-08 mr1369 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
vg0624805039 NA 1.41E-07 mr1690 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
vg0624805039 NA 1.14E-08 mr1776 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
vg0624805039 NA 8.70E-07 mr1781 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
vg0624805039 NA 1.72E-06 mr1886 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
vg0624805039 NA 2.30E-07 mr1979 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
vg0624805039 NA 2.48E-37 mr1075_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
vg0624805039 NA 5.88E-54 mr1124_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
vg0624805039 NA 3.00E-06 mr1723_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