\

Search for Variation information by Variation ID:

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

Detailed information for vg1209012982:

Variant ID: vg1209012982 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 9012982
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, A: 0.19, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTTCTGTCGGCGACTGGGTTTATCTCAAATTACAGCCGTTTGTGTAGCAGTCAGTTGTCACTCGCGCTAATCGCAGGTTGGCTTTTCGTTTTTATGGT[C/A]
CTTTTCAGGTTCTCTCTCTAGTTGGTGAAGTGGCTTACAAGTTGGCTTTACCAGCTACCAGTCTTATATACCCGGTGGTCCATGTCTCACAGCTTAAGAA

Reverse complement sequence

TTCTTAAGCTGTGAGACATGGACCACCGGGTATATAAGACTGGTAGCTGGTAAAGCCAACTTGTAAGCCACTTCACCAACTAGAGAGAGAACCTGAAAAG[G/T]
ACCATAAAAACGAAAAGCCAACCTGCGATTAGCGCGAGTGACAACTGACTGCTACACAAACGGCTGTAATTTGAGATAAACCCAGTCGCCGACAGAAAAT

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 45.60% 29.40% 0.44% 24.50% NA
All Indica  2759 12.50% 47.40% 0.72% 39.36% NA
All Japonica  1512 94.70% 3.90% 0.00% 1.39% NA
Aus  269 84.00% 1.10% 0.00% 14.87% NA
Indica I  595 15.10% 29.90% 0.84% 54.12% NA
Indica II  465 9.50% 49.20% 1.51% 39.78% NA
Indica III  913 8.40% 58.80% 0.22% 32.53% NA
Indica Intermediate  786 16.90% 46.40% 0.76% 35.88% NA
Temperate Japonica  767 92.80% 5.50% 0.00% 1.69% NA
Tropical Japonica  504 95.80% 3.40% 0.00% 0.79% NA
Japonica Intermediate  241 98.30% 0.00% 0.00% 1.66% NA
VI/Aromatic  96 91.70% 3.10% 1.04% 4.17% NA
Intermediate  90 74.40% 17.80% 0.00% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1209012982 C -> DEL N N silent_mutation Average:49.537; most accessible tissue: Minghui63 young leaf, score: 87.677 N N N N
vg1209012982 C -> A LOC_Os12g15780.1 downstream_gene_variant ; 3098.0bp to feature; MODIFIER silent_mutation Average:49.537; most accessible tissue: Minghui63 young leaf, score: 87.677 N N N N
vg1209012982 C -> A LOC_Os12g15790.1 intron_variant ; MODIFIER silent_mutation Average:49.537; most accessible tissue: Minghui63 young leaf, score: 87.677 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)
vg1209012982 C A -0.2 -0.39 -0.31 -0.04 -0.22 -0.15

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1209012982 NA 2.37E-10 mr1425 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
vg1209012982 NA 9.73E-08 mr1425 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
vg1209012982 NA 8.44E-06 mr1888 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
vg1209012982 2.13E-06 2.13E-06 mr1893 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
vg1209012982 NA 1.15E-07 mr1425_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
vg1209012982 NA 2.14E-07 mr1864_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