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Detailed information for vg1214986204:

Variant ID: vg1214986204 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 14986204
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


CAAACCTACAAAGAGATGTCGCACTCTCGCAGTGGTGGCGAACGGTTTACGACGCAAACCGACAAAGATGGACAAACCTACAAAGAGATGTCGCACTCTC[A/G]
CAGCGGTGGCGGACGGTTTACGGCGCAAACCGACAAAGATGGACAAACTAAGAGAAAACTAAAAGCAATATGAAAAACGATTCGATTGATTGATTGTAGA

Reverse complement sequence

TCTACAATCAATCAATCGAATCGTTTTTCATATTGCTTTTAGTTTTCTCTTAGTTTGTCCATCTTTGTCGGTTTGCGCCGTAAACCGTCCGCCACCGCTG[T/C]
GAGAGTGCGACATCTCTTTGTAGGTTTGTCCATCTTTGTCGGTTTGCGTCGTAAACCGTTCGCCACCACTGCGAGAGTGCGACATCTCTTTGTAGGTTTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 49.80% 10.60% 11.05% 28.48% NA
All Indica  2759 43.40% 2.80% 14.17% 39.58% NA
All Japonica  1512 50.00% 27.40% 7.87% 14.68% NA
Aus  269 96.70% 0.40% 0.74% 2.23% NA
Indica I  595 24.40% 5.70% 31.43% 38.49% NA
Indica II  465 51.60% 2.20% 6.45% 39.78% NA
Indica III  913 52.90% 0.50% 6.90% 39.65% NA
Indica Intermediate  786 42.00% 3.70% 14.12% 40.20% NA
Temperate Japonica  767 36.00% 47.60% 10.04% 6.39% NA
Tropical Japonica  504 68.50% 1.00% 4.17% 26.39% NA
Japonica Intermediate  241 56.00% 18.70% 8.71% 16.60% NA
VI/Aromatic  96 96.90% 1.00% 1.04% 1.04% NA
Intermediate  90 53.30% 8.90% 10.00% 27.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1214986204 A -> DEL N N silent_mutation Average:64.438; most accessible tissue: Zhenshan97 root, score: 91.723 N N N N
vg1214986204 A -> G LOC_Os12g25830.1 upstream_gene_variant ; 353.0bp to feature; MODIFIER silent_mutation Average:64.438; most accessible tissue: Zhenshan97 root, score: 91.723 N N N N
vg1214986204 A -> G LOC_Os12g25840.1 upstream_gene_variant ; 1999.0bp to feature; MODIFIER silent_mutation Average:64.438; most accessible tissue: Zhenshan97 root, score: 91.723 N N N N
vg1214986204 A -> G LOC_Os12g25830-LOC_Os12g25840 intergenic_region ; MODIFIER silent_mutation Average:64.438; most accessible tissue: Zhenshan97 root, score: 91.723 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)
vg1214986204 A G 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1214986204 NA 5.60E-06 mr1577 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
vg1214986204 2.65E-06 NA mr1022_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