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Detailed information for vg1208281892:

Variant ID: vg1208281892 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 8281892
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.62, A: 0.38, others allele: 0.00, population size: 69. )

Flanking Sequence (100 bp) in Reference Genome:


TTATGTGAGCATGTTTTAATTTAACCGCTAAACCGTACGTTACGTTTCTTTAAGCATTAAATAAATCTAATTATAAGTTATTAATATTTAATATGTCATC[C/A]
GCTTATAACCCAACTTGTTTTACATGCTTTTAAAAATTTTGAGCCCTCTATTGATTTAGCTGTTTTGAAAATTAAAGGACCCCAAATGTAACTGGGCACA

Reverse complement sequence

TGTGCCCAGTTACATTTGGGGTCCTTTAATTTTCAAAACAGCTAAATCAATAGAGGGCTCAAAATTTTTAAAAGCATGTAAAACAAGTTGGGTTATAAGC[G/T]
GATGACATATTAAATATTAATAACTTATAATTAGATTTATTTAATGCTTAAAGAAACGTAACGTACGGTTTAGCGGTTAAATTAAAACATGCTCACATAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 45.10% 27.90% 0.59% 26.47% NA
All Indica  2759 16.70% 45.90% 0.62% 36.79% NA
All Japonica  1512 94.90% 1.60% 0.20% 3.31% NA
Aus  269 44.20% 1.90% 2.97% 50.93% NA
Indica I  595 25.40% 30.10% 1.18% 43.36% NA
Indica II  465 12.30% 39.10% 0.65% 47.96% NA
Indica III  913 12.60% 59.00% 0.22% 28.15% NA
Indica Intermediate  786 17.40% 46.70% 0.64% 35.24% NA
Temperate Japonica  767 94.00% 0.70% 0.13% 5.22% NA
Tropical Japonica  504 95.00% 3.60% 0.40% 0.99% NA
Japonica Intermediate  241 97.50% 0.40% 0.00% 2.07% NA
VI/Aromatic  96 56.20% 2.10% 0.00% 41.67% NA
Intermediate  90 68.90% 21.10% 0.00% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1208281892 C -> DEL N N silent_mutation Average:46.255; most accessible tissue: Minghui63 flag leaf, score: 91.207 N N N N
vg1208281892 C -> A LOC_Os12g14510.1 upstream_gene_variant ; 1489.0bp to feature; MODIFIER silent_mutation Average:46.255; most accessible tissue: Minghui63 flag leaf, score: 91.207 N N N N
vg1208281892 C -> A LOC_Os12g14500.1 intron_variant ; MODIFIER silent_mutation Average:46.255; most accessible tissue: Minghui63 flag leaf, score: 91.207 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)
vg1208281892 C A 0.0 0.0 0.0 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1208281892 NA 1.42E-06 mr1851 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
vg1208281892 NA 4.32E-06 mr1539_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
vg1208281892 NA 1.93E-08 mr1540_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
vg1208281892 NA 2.44E-08 mr1732_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
vg1208281892 1.91E-06 1.09E-09 mr1910_2 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
vg1208281892 4.57E-07 1.49E-07 mr1910_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