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Detailed information for vg1127787917:

Variant ID: vg1127787917 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27787917
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.68, A: 0.32, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:


CAACACACATATCATGATATTAGGCAACAACCCATGACCGCTGTGTTGGTTCACCACCACCATGCACTTTCCCCACGCAGAGCTAGTTCAGGGCAAGGCA[A/G]
ATCCATCTATCCTCAGAAGAAATCTATCGTCTTCAACCACTACGACTGTGGGTGAGGCCCAAACCCAACGGGAGAGATCCTGTCGCGCCCCCTTTCTTGT

Reverse complement sequence

ACAAGAAAGGGGGCGCGACAGGATCTCTCCCGTTGGGTTTGGGCCTCACCCACAGTCGTAGTGGTTGAAGACGATAGATTTCTTCTGAGGATAGATGGAT[T/C]
TGCCTTGCCCTGAACTAGCTCTGCGTGGGGAAAGTGCATGGTGGTGGTGAACCAACACAGCGGTCATGGGTTGTTGCCTAATATCATGATATGTGTGTTG

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 50.10% 25.90% 1.65% 22.28% NA
All Indica  2759 45.80% 31.90% 1.63% 20.70% NA
All Japonica  1512 62.80% 19.30% 1.12% 16.73% NA
Aus  269 27.10% 7.80% 4.83% 60.22% NA
Indica I  595 58.50% 17.30% 2.18% 22.02% NA
Indica II  465 61.30% 11.80% 1.08% 25.81% NA
Indica III  913 28.40% 57.40% 0.77% 13.47% NA
Indica Intermediate  786 47.30% 25.10% 2.54% 25.06% NA
Temperate Japonica  767 63.90% 24.90% 1.17% 10.04% NA
Tropical Japonica  504 53.20% 17.50% 1.19% 28.17% NA
Japonica Intermediate  241 79.70% 5.40% 0.83% 14.11% NA
VI/Aromatic  96 31.20% 11.50% 2.08% 55.21% NA
Intermediate  90 58.90% 24.40% 1.11% 15.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1127787917 A -> DEL N N silent_mutation Average:51.669; most accessible tissue: Minghui63 flower, score: 88.423 N N N N
vg1127787917 A -> G LOC_Os11g45920.1 upstream_gene_variant ; 1935.0bp to feature; MODIFIER silent_mutation Average:51.669; most accessible tissue: Minghui63 flower, score: 88.423 N N N N
vg1127787917 A -> G LOC_Os11g45924.1 downstream_gene_variant ; 1701.0bp to feature; MODIFIER silent_mutation Average:51.669; most accessible tissue: Minghui63 flower, score: 88.423 N N N N
vg1127787917 A -> G LOC_Os11g45920-LOC_Os11g45924 intergenic_region ; MODIFIER silent_mutation Average:51.669; most accessible tissue: Minghui63 flower, score: 88.423 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)
vg1127787917 A G 0.08 0.02 0.03 0.16 0.16 0.14

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127787917 4.75E-07 4.68E-10 mr1133 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
vg1127787917 4.48E-07 7.12E-08 mr1667 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
vg1127787917 9.30E-06 2.12E-09 mr1133_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
vg1127787917 NA 6.03E-06 mr1594_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
vg1127787917 9.21E-06 5.20E-08 mr1667_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