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Detailed information for vg1227259456:

Variant ID: vg1227259456 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 27259456
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.04, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


CAAAGCAGGGGCAACAACCCTACAGGAGTTTGGAATCCTGGGAAATATCACTTAGCTCTTTTTCTTTTTTGCGGGCTAGTCTTTTTCCTCGGCTAACCCT[G/A]
TATATACCCTTGTTTATTTTTCTCCTGCTCTATTAATATACACAAGACAAAGCTTTTGCCTTTCTTCAAAAAAAAAACTTGCAAATTAAAAAGATGTTGA

Reverse complement sequence

TCAACATCTTTTTAATTTGCAAGTTTTTTTTTTGAAGAAAGGCAAAAGCTTTGTCTTGTGTATATTAATAGAGCAGGAGAAAAATAAACAAGGGTATATA[C/T]
AGGGTTAGCCGAGGAAAAAGACTAGCCCGCAAAAAAGAAAAAGAGCTAAGTGATATTTCCCAGGATTCCAAACTCCTGTAGGGTTGTTGCCCCTGCTTTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.80% 45.80% 0.40% 0.00% NA
All Indica  2759 89.90% 9.50% 0.65% 0.00% NA
All Japonica  1512 0.60% 99.30% 0.07% 0.00% NA
Aus  269 3.00% 97.00% 0.00% 0.00% NA
Indica I  595 77.80% 21.50% 0.67% 0.00% NA
Indica II  465 95.70% 3.00% 1.29% 0.00% NA
Indica III  913 94.00% 6.00% 0.00% 0.00% NA
Indica Intermediate  786 90.70% 8.30% 1.02% 0.00% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 0.80% 99.20% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.30% 0.41% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 45.60% 54.40% 0.00% 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
vg1227259456 G -> A LOC_Os12g43930.1 upstream_gene_variant ; 4263.0bp to feature; MODIFIER silent_mutation Average:58.031; most accessible tissue: Minghui63 root, score: 93.296 N N N N
vg1227259456 G -> A LOC_Os12g43900.1 downstream_gene_variant ; 2814.0bp to feature; MODIFIER silent_mutation Average:58.031; most accessible tissue: Minghui63 root, score: 93.296 N N N N
vg1227259456 G -> A LOC_Os12g43910.1 downstream_gene_variant ; 950.0bp to feature; MODIFIER silent_mutation Average:58.031; most accessible tissue: Minghui63 root, score: 93.296 N N N N
vg1227259456 G -> A LOC_Os12g43910-LOC_Os12g43930 intergenic_region ; MODIFIER silent_mutation Average:58.031; most accessible tissue: Minghui63 root, score: 93.296 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)
vg1227259456 G A -0.03 -0.01 -0.02 -0.01 -0.02 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1227259456 NA 1.84E-25 mr1024 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
vg1227259456 1.45E-06 9.73E-07 mr1134 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
vg1227259456 5.79E-07 1.32E-07 mr1135 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
vg1227259456 NA 2.66E-09 mr1151 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
vg1227259456 NA 1.19E-15 mr1164 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
vg1227259456 NA 7.83E-28 mr1221 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
vg1227259456 NA 1.19E-07 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
vg1227259456 2.49E-06 1.32E-06 mr1504 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
vg1227259456 NA 2.16E-23 mr1571 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
vg1227259456 NA 2.94E-23 mr1580 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
vg1227259456 NA 5.71E-06 mr1672 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
vg1227259456 NA 4.81E-29 mr1793 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
vg1227259456 NA 1.11E-17 mr1825 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
vg1227259456 NA 5.69E-12 mr1151_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
vg1227259456 NA 3.67E-07 mr1302_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
vg1227259456 NA 2.02E-06 mr1488_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
vg1227259456 6.37E-06 5.39E-06 mr1504_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
vg1227259456 NA 8.88E-10 mr1506_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
vg1227259456 NA 2.67E-07 mr1604_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
vg1227259456 NA 4.24E-07 mr1824_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
vg1227259456 NA 7.42E-25 mr1943_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