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Detailed information for vg0521819187:

Variant ID: vg0521819187 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 21819187
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.60, T: 0.40, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


ACGCATAAAATTTTAATCATGTTTTATCATCTAACAACAATAAAAATACGAATTATAAAAAAATTTATATAAGACGGATAGTCAAAGTTAGACACGGAAA[C/T]
TCAGGGTTTGCTTTATTTTTTTAGGACGGAGGGAGTACATCGGGGCGAGCTGCAGCTTTTCACGACTCCGACACGGTGACAGACGCGCGCGGATGCGATG

Reverse complement sequence

CATCGCATCCGCGCGCGTCTGTCACCGTGTCGGAGTCGTGAAAAGCTGCAGCTCGCCCCGATGTACTCCCTCCGTCCTAAAAAAATAAAGCAAACCCTGA[G/A]
TTTCCGTGTCTAACTTTGACTATCCGTCTTATATAAATTTTTTTATAATTCGTATTTTTATTGTTGTTAGATGATAAAACATGATTAAAATTTTATGCGT

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 60.90% 38.90% 0.19% 0.00% NA
All Indica  2759 39.10% 60.70% 0.25% 0.00% NA
All Japonica  1512 99.40% 0.60% 0.00% 0.00% NA
Aus  269 56.10% 43.50% 0.37% 0.00% NA
Indica I  595 55.50% 44.00% 0.50% 0.00% NA
Indica II  465 16.10% 83.70% 0.22% 0.00% NA
Indica III  913 43.70% 56.30% 0.00% 0.00% NA
Indica Intermediate  786 34.90% 64.80% 0.38% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 57.80% 41.10% 1.11% 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
vg0521819187 C -> T LOC_Os05g37280.1 upstream_gene_variant ; 3031.0bp to feature; MODIFIER silent_mutation Average:90.233; most accessible tissue: Minghui63 panicle, score: 98.937 N N N N
vg0521819187 C -> T LOC_Os05g37290.1 upstream_gene_variant ; 2410.0bp to feature; MODIFIER silent_mutation Average:90.233; most accessible tissue: Minghui63 panicle, score: 98.937 N N N N
vg0521819187 C -> T LOC_Os05g37300.1 downstream_gene_variant ; 4663.0bp to feature; MODIFIER silent_mutation Average:90.233; most accessible tissue: Minghui63 panicle, score: 98.937 N N N N
vg0521819187 C -> T LOC_Os05g37280-LOC_Os05g37290 intergenic_region ; MODIFIER silent_mutation Average:90.233; most accessible tissue: Minghui63 panicle, score: 98.937 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)
vg0521819187 C T 0.0 0.1 0.08 0.05 0.04 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0521819187 NA 3.31E-07 mr1044 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
vg0521819187 NA 4.77E-07 mr1115 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
vg0521819187 NA 3.57E-07 mr1265 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
vg0521819187 NA 1.05E-09 mr1352 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
vg0521819187 NA 4.42E-07 mr1352 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
vg0521819187 1.96E-06 1.96E-06 mr1359 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
vg0521819187 NA 9.77E-06 mr1528 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
vg0521819187 NA 2.27E-06 mr1564 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
vg0521819187 NA 3.59E-06 mr1611 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
vg0521819187 NA 2.77E-06 mr1622 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
vg0521819187 NA 8.91E-08 mr1659 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
vg0521819187 NA 8.65E-06 mr1716 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
vg0521819187 NA 6.40E-08 mr1735 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
vg0521819187 NA 2.43E-06 mr1737 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
vg0521819187 NA 9.63E-06 mr1740 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
vg0521819187 NA 4.31E-07 mr1992 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
vg0521819187 NA 6.97E-06 mr1236_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
vg0521819187 NA 4.80E-12 mr1830_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
vg0521819187 NA 5.26E-08 mr1830_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