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Detailed information for vg1225798168:

Variant ID: vg1225798168 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 25798168
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, T: 0.02, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


TGCTGCTTGAAAAATCTTCTCCTTGGGATTGATTGATCGATCGATCAAATGGATATCATGATTAGCTTGTGATGAACTCCAGTATGTATACCACTTGTGA[T/A]
CTGATGTGCTGCTGCTCCTGCAGGACTGCAGAAGGAATATTTCCAGCAGGAGAGGTGCAGAAACCCCGGGCTACTGTCTATTACTCCACCCTTGACTGGA

Reverse complement sequence

TCCAGTCAAGGGTGGAGTAATAGACAGTAGCCCGGGGTTTCTGCACCTCTCCTGCTGGAAATATTCCTTCTGCAGTCCTGCAGGAGCAGCAGCACATCAG[A/T]
TCACAAGTGGTATACATACTGGAGTTCATCACAAGCTAATCATGATATCCATTTGATCGATCGATCAATCAATCCCAAGGAGAAGATTTTTCAAGCAGCA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.30% 34.80% 0.89% 0.00% NA
All Indica  2759 50.60% 48.00% 1.41% 0.00% NA
All Japonica  1512 99.30% 0.60% 0.07% 0.00% NA
Aus  269 1.90% 97.80% 0.37% 0.00% NA
Indica I  595 54.30% 42.40% 3.36% 0.00% NA
Indica II  465 54.80% 43.40% 1.72% 0.00% NA
Indica III  913 51.60% 48.30% 0.11% 0.00% NA
Indica Intermediate  786 44.10% 54.60% 1.27% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.20% 0.41% 0.00% NA
VI/Aromatic  96 67.70% 31.20% 1.04% 0.00% NA
Intermediate  90 77.80% 22.20% 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
vg1225798168 T -> A LOC_Os12g41680.1 upstream_gene_variant ; 2776.0bp to feature; MODIFIER silent_mutation Average:93.987; most accessible tissue: Zhenshan97 flower, score: 98.613 N N N N
vg1225798168 T -> A LOC_Os12g41670.1 downstream_gene_variant ; 1783.0bp to feature; MODIFIER silent_mutation Average:93.987; most accessible tissue: Zhenshan97 flower, score: 98.613 N N N N
vg1225798168 T -> A LOC_Os12g41670-LOC_Os12g41680 intergenic_region ; MODIFIER silent_mutation Average:93.987; most accessible tissue: Zhenshan97 flower, score: 98.613 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)
vg1225798168 T A 0.0 0.0 0.0 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1225798168 NA 4.85E-06 mr1207 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
vg1225798168 NA 9.00E-07 mr1209 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
vg1225798168 NA 3.93E-09 mr1222 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
vg1225798168 NA 1.42E-06 mr1278 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
vg1225798168 NA 6.50E-09 mr1302 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
vg1225798168 NA 1.48E-10 mr1307 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
vg1225798168 NA 1.87E-06 mr1315 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
vg1225798168 NA 1.96E-06 mr1389 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
vg1225798168 NA 6.07E-08 mr1392 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
vg1225798168 NA 2.28E-07 mr1420 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
vg1225798168 NA 9.10E-06 mr1422 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
vg1225798168 NA 3.64E-07 mr1424 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
vg1225798168 NA 6.76E-09 mr1442 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
vg1225798168 NA 3.93E-08 mr1488 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
vg1225798168 9.45E-07 9.44E-07 mr1562 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
vg1225798168 NA 3.42E-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
vg1225798168 NA 1.98E-06 mr1681 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
vg1225798168 NA 7.93E-06 mr1741 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
vg1225798168 NA 2.65E-09 mr1806 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
vg1225798168 NA 1.37E-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