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Detailed information for vg0600529931:

Variant ID: vg0600529931 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 529931
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


GGGGATTTCTTTTGTAAAAATCAGCCCACCACTTCTGTTCTGGCCTAGCTAGCTTAGCATGCAGTGATGTGGAACCCACCCTTGCAATCCCATCTGGGCC[C/T]
ATGACAAGTTAGTTACTTAGAGCACCCGCAATGGTAAAGTAAGGTGTTATCTATAAAACATGTACATCTCAGCAATAGACTAGATTAATAGTAAACCACT

Reverse complement sequence

AGTGGTTTACTATTAATCTAGTCTATTGCTGAGATGTACATGTTTTATAGATAACACCTTACTTTACCATTGCGGGTGCTCTAAGTAACTAACTTGTCAT[G/A]
GGCCCAGATGGGATTGCAAGGGTGGGTTCCACATCACTGCATGCTAAGCTAGCTAGGCCAGAACAGAAGTGGTGGGCTGATTTTTACAAAAGAAATCCCC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.70% 35.00% 0.28% 0.06% NA
All Indica  2759 41.70% 57.80% 0.36% 0.11% NA
All Japonica  1512 97.80% 2.10% 0.07% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 53.90% 45.00% 0.50% 0.50% NA
Indica II  465 55.50% 43.90% 0.65% 0.00% NA
Indica III  913 19.90% 80.10% 0.00% 0.00% NA
Indica Intermediate  786 49.50% 50.00% 0.51% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 94.00% 5.80% 0.20% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 74.40% 23.30% 2.22% 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
vg0600529931 C -> T LOC_Os06g01934.1 3_prime_UTR_variant ; 247.0bp to feature; MODIFIER silent_mutation Average:81.586; most accessible tissue: Minghui63 flag leaf, score: 95.372 N N N N
vg0600529931 C -> T LOC_Os06g01950.1 downstream_gene_variant ; 603.0bp to feature; MODIFIER silent_mutation Average:81.586; most accessible tissue: Minghui63 flag leaf, score: 95.372 N N N N
vg0600529931 C -> T LOC_Os06g01960.1 downstream_gene_variant ; 3543.0bp to feature; MODIFIER silent_mutation Average:81.586; most accessible tissue: Minghui63 flag leaf, score: 95.372 N N N N
vg0600529931 C -> DEL N N silent_mutation Average:81.586; most accessible tissue: Minghui63 flag leaf, score: 95.372 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)
vg0600529931 C T -0.33 -0.32 -0.22 -0.23 -0.26 -0.25

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0600529931 NA 1.83E-07 mr1086 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
vg0600529931 NA 3.65E-07 mr1104 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
vg0600529931 NA 3.31E-06 mr1155 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
vg0600529931 NA 2.91E-06 mr1246 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
vg0600529931 3.16E-06 3.16E-06 mr1770 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
vg0600529931 NA 5.63E-06 mr1092_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
vg0600529931 NA 4.02E-06 mr1152_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