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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1215665438:

Variant ID: vg1215665438 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 15665438
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, G: 0.04, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


ATCAAACAGGAGACAGCAATCAGCAACATTGGCCATCAAAAGGCTGGGGAATGAGGCAGTGGATGGGCCATGAATTTTTAATCGAGCAGAATCCCTAGGC[C/G]
CATATGTCGTTGACTGGATCACCAGGCCCGGCCCATATATAGCTGACCCGACGAAGTCACAACTGCATTTGGATCGCAGCCGATGCGAGCGGCCCAATTT

Reverse complement sequence

AAATTGGGCCGCTCGCATCGGCTGCGATCCAAATGCAGTTGTGACTTCGTCGGGTCAGCTATATATGGGCCGGGCCTGGTGATCCAGTCAACGACATATG[G/C]
GCCTAGGGATTCTGCTCGATTAAAAATTCATGGCCCATCCACTGCCTCATTCCCCAGCCTTTTGATGGCCAATGTTGCTGATTGCTGTCTCCTGTTTGAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 41.60% 23.10% 0.47% 34.83% NA
All Indica  2759 16.90% 38.40% 0.54% 44.18% NA
All Japonica  1512 77.10% 1.10% 0.46% 21.36% NA
Aus  269 90.70% 0.40% 0.00% 8.92% NA
Indica I  595 18.70% 71.80% 0.17% 9.41% NA
Indica II  465 20.20% 16.60% 0.86% 62.37% NA
Indica III  913 11.00% 26.40% 0.66% 61.99% NA
Indica Intermediate  786 20.40% 40.10% 0.51% 39.06% NA
Temperate Japonica  767 94.30% 0.50% 0.26% 4.95% NA
Tropical Japonica  504 54.00% 1.60% 0.79% 43.65% NA
Japonica Intermediate  241 71.00% 1.70% 0.41% 26.97% NA
VI/Aromatic  96 38.50% 2.10% 0.00% 59.38% NA
Intermediate  90 60.00% 14.40% 0.00% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1215665438 C -> DEL N N silent_mutation Average:48.997; most accessible tissue: Callus, score: 97.146 N N N N
vg1215665438 C -> G LOC_Os12g26720.1 upstream_gene_variant ; 2741.0bp to feature; MODIFIER silent_mutation Average:48.997; most accessible tissue: Callus, score: 97.146 N N N N
vg1215665438 C -> G LOC_Os12g26740.1 upstream_gene_variant ; 4400.0bp to feature; MODIFIER silent_mutation Average:48.997; most accessible tissue: Callus, score: 97.146 N N N N
vg1215665438 C -> G LOC_Os12g26720-LOC_Os12g26740 intergenic_region ; MODIFIER silent_mutation Average:48.997; most accessible tissue: Callus, score: 97.146 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)
vg1215665438 C G -0.43 -0.53 -0.39 -0.4 -0.33 -0.36

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1215665438 NA 1.71E-06 mr1176 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
vg1215665438 NA 9.17E-06 mr1568 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
vg1215665438 NA 1.73E-11 mr1610 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
vg1215665438 NA 1.08E-06 mr1610 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