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Detailed information for vg1126497827:

Variant ID: vg1126497827 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26497827
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.78, A: 0.24, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:


TCACTTAGCGCCCCCGGCCGAACCGGCAAAGGGGGGCCTGCGCGGTCTCCCGGTGAGGAGCCCCACGCTCCGTCACCATCGGTATCTCAATGACATATAG[G/A]
ACCCACATGAGTCAATGACATGTGGTTCAAGATGGCATATCTCAAATTTTGCAAAATTATAATGGCATGGTTTCAATTTTCCCTTGATTTTTTTACTCTC

Reverse complement sequence

GAGAGTAAAAAAATCAAGGGAAAATTGAAACCATGCCATTATAATTTTGCAAAATTTGAGATATGCCATCTTGAACCACATGTCATTGACTCATGTGGGT[C/T]
CTATATGTCATTGAGATACCGATGGTGACGGAGCGTGGGGCTCCTCACCGGGAGACCGCGCAGGCCCCCCTTTGCCGGTTCGGCCGGGGGCGCTAAGTGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.30% 31.30% 1.29% 8.17% NA
All Indica  2759 52.70% 32.60% 1.63% 13.08% NA
All Japonica  1512 65.10% 33.70% 0.66% 0.60% NA
Aus  269 82.50% 15.20% 1.49% 0.74% NA
Indica I  595 43.20% 17.10% 5.88% 33.78% NA
Indica II  465 64.30% 19.60% 0.22% 15.91% NA
Indica III  913 50.40% 47.80% 0.11% 1.75% NA
Indica Intermediate  786 55.60% 34.50% 1.02% 8.91% NA
Temperate Japonica  767 38.70% 59.30% 0.78% 1.17% NA
Tropical Japonica  504 96.20% 3.40% 0.40% 0.00% NA
Japonica Intermediate  241 83.80% 15.40% 0.83% 0.00% NA
VI/Aromatic  96 94.80% 3.10% 0.00% 2.08% NA
Intermediate  90 57.80% 26.70% 2.22% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1126497827 G -> A LOC_Os11g43880.1 upstream_gene_variant ; 356.0bp to feature; MODIFIER silent_mutation Average:59.69; most accessible tissue: Minghui63 flag leaf, score: 88.459 N N N N
vg1126497827 G -> A LOC_Os11g43890.1 upstream_gene_variant ; 3791.0bp to feature; MODIFIER silent_mutation Average:59.69; most accessible tissue: Minghui63 flag leaf, score: 88.459 N N N N
vg1126497827 G -> A LOC_Os11g43870.1 downstream_gene_variant ; 2511.0bp to feature; MODIFIER silent_mutation Average:59.69; most accessible tissue: Minghui63 flag leaf, score: 88.459 N N N N
vg1126497827 G -> A LOC_Os11g43880-LOC_Os11g43890 intergenic_region ; MODIFIER silent_mutation Average:59.69; most accessible tissue: Minghui63 flag leaf, score: 88.459 N N N N
vg1126497827 G -> DEL N N silent_mutation Average:59.69; most accessible tissue: Minghui63 flag leaf, score: 88.459 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)
vg1126497827 G A -0.04 -0.03 -0.03 -0.02 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126497827 NA 1.25E-07 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
vg1126497827 NA 1.18E-06 mr1561 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
vg1126497827 1.45E-06 1.21E-08 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
vg1126497827 1.02E-07 8.40E-12 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
vg1126497827 NA 6.46E-06 mr1908 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
vg1126497827 NA 1.82E-08 mr1010_2 Jap_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
vg1126497827 9.38E-11 3.59E-15 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
vg1126497827 NA 1.09E-06 mr1380_2 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
vg1126497827 8.29E-07 4.36E-09 mr1380_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
vg1126497827 NA 3.05E-07 mr1561_2 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
vg1126497827 1.53E-06 1.78E-09 mr1561_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
vg1126497827 NA 2.17E-06 mr1582_2 Jap_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
vg1126497827 6.84E-07 6.99E-10 mr1875_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
vg1126497827 4.65E-06 7.58E-09 mr1875_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
vg1126497827 2.97E-07 7.81E-10 mr1908_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
vg1126497827 4.02E-07 7.54E-10 mr1908_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
vg1126497827 3.01E-06 1.96E-07 mr1996_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
vg1126497827 8.76E-08 2.78E-09 mr1996_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