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Detailed information for vg1127281051:

Variant ID: vg1127281051 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27281051
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.85, A: 0.14, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:


ATTCAAGGGCGCAGCTAGTTGACTAGTTCCACATCATGGAATCTTGAAGCCAACAGTAAAGTAATCACATAGAAGTAAACTGTAGATCAATCACATGGAA[A/G]
TAAACTGTGAACTAATCACATCGACTAGACAAGTGGACAAGCACAAAACGTTGGGTTGTGGAGCATAGACAAGTGGACAATAACTCAAAATTGGGTCAGC

Reverse complement sequence

GCTGACCCAATTTTGAGTTATTGTCCACTTGTCTATGCTCCACAACCCAACGTTTTGTGCTTGTCCACTTGTCTAGTCGATGTGATTAGTTCACAGTTTA[T/C]
TTCCATGTGATTGATCTACAGTTTACTTCTATGTGATTACTTTACTGTTGGCTTCAAGATTCCATGATGTGGAACTAGTCAACTAGCTGCGCCCTTGAAT

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 32.20% 14.20% 1.18% 52.33% NA
All Indica  2759 42.10% 7.20% 1.09% 49.62% NA
All Japonica  1512 14.50% 28.80% 1.12% 55.56% NA
Aus  269 8.90% 8.60% 3.35% 79.18% NA
Indica I  595 51.30% 14.10% 1.85% 32.77% NA
Indica II  465 30.10% 5.60% 1.51% 62.80% NA
Indica III  913 45.50% 2.20% 0.44% 51.92% NA
Indica Intermediate  786 38.30% 8.80% 1.02% 51.91% NA
Temperate Japonica  767 8.60% 49.00% 1.04% 41.33% NA
Tropical Japonica  504 23.40% 5.60% 1.19% 69.84% NA
Japonica Intermediate  241 14.50% 13.30% 1.24% 70.95% NA
VI/Aromatic  96 76.00% 0.00% 0.00% 23.96% NA
Intermediate  90 52.20% 16.70% 0.00% 31.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1127281051 A -> DEL N N silent_mutation Average:81.244; most accessible tissue: Zhenshan97 young leaf, score: 96.081 N N N N
vg1127281051 A -> G LOC_Os11g45090.1 upstream_gene_variant ; 1181.0bp to feature; MODIFIER silent_mutation Average:81.244; most accessible tissue: Zhenshan97 young leaf, score: 96.081 N N N N
vg1127281051 A -> G LOC_Os11g45070.1 downstream_gene_variant ; 4709.0bp to feature; MODIFIER silent_mutation Average:81.244; most accessible tissue: Zhenshan97 young leaf, score: 96.081 N N N N
vg1127281051 A -> G LOC_Os11g45080.1 intron_variant ; MODIFIER silent_mutation Average:81.244; most accessible tissue: Zhenshan97 young leaf, score: 96.081 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)
vg1127281051 A G 0.15 0.05 0.0 0.0 0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127281051 3.61E-06 NA mr1118_2 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
vg1127281051 4.61E-06 1.08E-06 mr1238_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
vg1127281051 4.03E-06 NA mr1242_2 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
vg1127281051 NA 4.42E-06 mr1484_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