Search for Variation information by Variation ID:

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

Detailed information for vg1223902919:

Variant ID: vg1223902919 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 23902919
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.71, G: 0.29, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


ACAAAGGTGAATAATTAATCCAAAAATCTTCTTTTGTCACAGCTAGATTAACAAATACTCCAGTAACAACCAACAGGTTACTAGTTGTAGTACTAGTACT[A/G]
GAGAATAAAAAATGGAAATAGGTAGGGGGTTGTACTGCAAATTGGGAATTTATTATGTGGGGCTACGTGGATGGGAAAGCACTATTTATGACTTTATTCT

Reverse complement sequence

AGAATAAAGTCATAAATAGTGCTTTCCCATCCACGTAGCCCCACATAATAAATTCCCAATTTGCAGTACAACCCCCTACCTATTTCCATTTTTTATTCTC[T/C]
AGTACTAGTACTACAACTAGTAACCTGTTGGTTGTTACTGGAGTATTTGTTAATCTAGCTGTGACAAAAGAAGATTTTTGGATTAATTATTCACCTTTGT

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 57.00% 42.70% 0.11% 0.25% NA
All Indica  2759 37.20% 62.20% 0.18% 0.43% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 4.80% 95.20% 0.00% 0.00% NA
Indica I  595 10.40% 88.90% 0.34% 0.34% NA
Indica II  465 41.90% 57.80% 0.00% 0.22% NA
Indica III  913 46.20% 53.00% 0.11% 0.66% NA
Indica Intermediate  786 44.30% 55.10% 0.25% 0.38% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 89.60% 10.40% 0.00% 0.00% NA
Intermediate  90 68.90% 31.10% 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
vg1223902919 A -> DEL N N silent_mutation Average:95.775; most accessible tissue: Minghui63 young leaf, score: 98.023 N N N N
vg1223902919 A -> G LOC_Os12g38870.1 upstream_gene_variant ; 4615.0bp to feature; MODIFIER silent_mutation Average:95.775; most accessible tissue: Minghui63 young leaf, score: 98.023 N N N N
vg1223902919 A -> G LOC_Os12g38870.2 upstream_gene_variant ; 4615.0bp to feature; MODIFIER silent_mutation Average:95.775; most accessible tissue: Minghui63 young leaf, score: 98.023 N N N N
vg1223902919 A -> G LOC_Os12g38870-LOC_Os12g38880 intergenic_region ; MODIFIER silent_mutation Average:95.775; most accessible tissue: Minghui63 young leaf, score: 98.023 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)
vg1223902919 A G -0.01 0.0 0.0 0.03 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1223902919 NA 7.41E-15 mr1874 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
vg1223902919 4.79E-06 NA mr1913_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