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Detailed information for vg1126259017:

Variant ID: vg1126259017 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26259017
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.80, A: 0.20, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


GAATGCGTATGTGATTTGTGATTGCCTCCTCCGTATTATTCTGTCTAGGAGCATGGTAGTTGCTATCGCTTGGATCTGGGGGGGTTTCGTTTTCTTAATT[C/A]
GTGAATTTTAGTTTGCGGTATTTCAATTATGGATCAGGAAGTTTGATGAAAGAGAAGATGTATTTGGAATTTTGGATGTCCCTTTTTCTCTACAGATCTG

Reverse complement sequence

CAGATCTGTAGAGAAAAAGGGACATCCAAAATTCCAAATACATCTTCTCTTTCATCAAACTTCCTGATCCATAATTGAAATACCGCAAACTAAAATTCAC[G/T]
AATTAAGAAAACGAAACCCCCCCAGATCCAAGCGATAGCAACTACCATGCTCCTAGACAGAATAATACGGAGGAGGCAATCACAAATCACATACGCATTC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 49.70% 35.60% 0.44% 14.22% NA
All Indica  2759 51.70% 33.30% 0.29% 14.68% NA
All Japonica  1512 47.30% 35.30% 0.73% 16.67% NA
Aus  269 55.40% 44.60% 0.00% 0.00% NA
Indica I  595 34.80% 29.60% 0.67% 34.96% NA
Indica II  465 20.60% 61.90% 0.65% 16.77% NA
Indica III  913 76.80% 15.60% 0.11% 7.56% NA
Indica Intermediate  786 53.70% 39.90% 0.00% 6.36% NA
Temperate Japonica  767 55.70% 41.60% 0.65% 2.09% NA
Tropical Japonica  504 35.10% 20.40% 0.99% 43.45% NA
Japonica Intermediate  241 46.10% 46.50% 0.41% 7.05% NA
VI/Aromatic  96 21.90% 78.10% 0.00% 0.00% NA
Intermediate  90 42.20% 38.90% 2.22% 16.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1126259017 C -> A LOC_Os11g43510.1 upstream_gene_variant ; 4709.0bp to feature; MODIFIER silent_mutation Average:84.855; most accessible tissue: Zhenshan97 panicle, score: 90.661 N N N N
vg1126259017 C -> A LOC_Os11g43480.1 downstream_gene_variant ; 1909.0bp to feature; MODIFIER silent_mutation Average:84.855; most accessible tissue: Zhenshan97 panicle, score: 90.661 N N N N
vg1126259017 C -> A LOC_Os11g43500.1 downstream_gene_variant ; 1125.0bp to feature; MODIFIER silent_mutation Average:84.855; most accessible tissue: Zhenshan97 panicle, score: 90.661 N N N N
vg1126259017 C -> A LOC_Os11g43490.1 intron_variant ; MODIFIER silent_mutation Average:84.855; most accessible tissue: Zhenshan97 panicle, score: 90.661 N N N N
vg1126259017 C -> DEL N N silent_mutation Average:84.855; most accessible tissue: Zhenshan97 panicle, score: 90.661 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)
vg1126259017 C A 0.01 0.01 0.02 0.01 0.02 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126259017 7.60E-06 1.22E-09 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
vg1126259017 NA 2.40E-08 mr1191 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
vg1126259017 NA 1.37E-11 mr1644 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
vg1126259017 NA 2.50E-07 mr1667 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
vg1126259017 6.35E-06 7.37E-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
vg1126259017 NA 4.25E-11 mr1191_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
vg1126259017 2.09E-06 3.37E-08 mr1667_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