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Detailed information for vg1125589582:

Variant ID: vg1125589582 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25589582
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


ATTAATTAGTACCTCTTCTTCATTAAATTATGATTTTTTAAAATCATCCAACCTCAAGATGTCTAATTCTATTGGGTGCATACATTTTATTTATTAGGGT[G/A]
ATATAAATTAGGAGATGATAATAATTATTTCTTGGTCTTTGGGTTAAGAGTGGTTGTGCCTTATATTTTGGAACGGAGGGAGTACATTGGTTATAGATAA

Reverse complement sequence

TTATCTATAACCAATGTACTCCCTCCGTTCCAAAATATAAGGCACAACCACTCTTAACCCAAAGACCAAGAAATAATTATTATCATCTCCTAATTTATAT[C/T]
ACCCTAATAAATAAAATGTATGCACCCAATAGAATTAGACATCTTGAGGTTGGATGATTTTAAAAAATCATAATTTAATGAAGAAGAGGTACTAATTAAT

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 85.50% 14.40% 0.08% 0.00% NA
All Indica  2759 85.10% 14.80% 0.07% 0.00% NA
All Japonica  1512 89.30% 10.70% 0.00% 0.00% NA
Aus  269 79.60% 20.40% 0.00% 0.00% NA
Indica I  595 53.40% 46.60% 0.00% 0.00% NA
Indica II  465 96.80% 3.00% 0.22% 0.00% NA
Indica III  913 97.70% 2.30% 0.00% 0.00% NA
Indica Intermediate  786 87.70% 12.20% 0.13% 0.00% NA
Temperate Japonica  767 97.80% 2.20% 0.00% 0.00% NA
Tropical Japonica  504 84.30% 15.70% 0.00% 0.00% NA
Japonica Intermediate  241 72.60% 27.40% 0.00% 0.00% NA
VI/Aromatic  96 56.20% 43.80% 0.00% 0.00% NA
Intermediate  90 84.40% 13.30% 2.22% 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
vg1125589582 G -> A LOC_Os11g42480.1 upstream_gene_variant ; 4212.0bp to feature; MODIFIER silent_mutation Average:89.175; most accessible tissue: Minghui63 flag leaf, score: 98.704 N N N N
vg1125589582 G -> A LOC_Os11g42490.1 upstream_gene_variant ; 308.0bp to feature; MODIFIER silent_mutation Average:89.175; most accessible tissue: Minghui63 flag leaf, score: 98.704 N N N N
vg1125589582 G -> A LOC_Os11g42500.1 upstream_gene_variant ; 4173.0bp to feature; MODIFIER silent_mutation Average:89.175; most accessible tissue: Minghui63 flag leaf, score: 98.704 N N N N
vg1125589582 G -> A LOC_Os11g42480-LOC_Os11g42490 intergenic_region ; MODIFIER silent_mutation Average:89.175; most accessible tissue: Minghui63 flag leaf, score: 98.704 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)
vg1125589582 G A 0.0 0.0 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
vg1125589582 2.65E-12 NA mr1191 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
vg1125589582 4.07E-12 1.16E-09 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
vg1125589582 NA 2.19E-06 mr1511 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
vg1125589582 3.67E-17 1.26E-10 mr1644 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
vg1125589582 1.88E-16 1.45E-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
vg1125589582 NA 8.35E-06 mr1074_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
vg1125589582 1.30E-17 NA mr1191_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
vg1125589582 2.54E-18 2.23E-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