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Detailed information for vg1125153506:

Variant ID: vg1125153506 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25153506
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:


TTCTAGGGTTCGGTGGCTCGAGCGGTGGAGGCGGCGGGCGCGAGGTGGGAGAGCACGCGAGGGGAACGGGTCGGTTTATATAGAGAAAGGACACTGACGT[G/A]
TGGGGCCCGGGACTCGGGTGAGAGCCACGTCGGTTTTTGGAGGCGGTGGCGGTGGCGGCGTCTGCAACCGTCGCGAAGTCGTGTTTTGAGTTTAAGTCGG

Reverse complement sequence

CCGACTTAAACTCAAAACACGACTTCGCGACGGTTGCAGACGCCGCCACCGCCACCGCCTCCAAAAACCGACGTGGCTCTCACCCGAGTCCCGGGCCCCA[C/T]
ACGTCAGTGTCCTTTCTCTATATAAACCGACCCGTTCCCCTCGCGTGCTCTCCCACCTCGCGCCCGCCGCCTCCACCGCTCGAGCCACCGAACCCTAGAA

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 63.70% 36.10% 0.17% 0.00% NA
All Indica  2759 61.10% 38.60% 0.25% 0.00% NA
All Japonica  1512 71.60% 28.40% 0.00% 0.00% NA
Aus  269 32.70% 67.30% 0.00% 0.00% NA
Indica I  595 67.10% 32.40% 0.50% 0.00% NA
Indica II  465 60.20% 39.60% 0.22% 0.00% NA
Indica III  913 61.10% 38.70% 0.22% 0.00% NA
Indica Intermediate  786 57.30% 42.60% 0.13% 0.00% NA
Temperate Japonica  767 94.00% 6.00% 0.00% 0.00% NA
Tropical Japonica  504 36.70% 63.30% 0.00% 0.00% NA
Japonica Intermediate  241 73.40% 26.60% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 66.70% 32.20% 1.11% 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
vg1125153506 G -> A LOC_Os11g41820.1 upstream_gene_variant ; 50.0bp to feature; MODIFIER silent_mutation Average:99.22; most accessible tissue: Callus, score: 99.802 N N N N
vg1125153506 G -> A LOC_Os11g41820.2 upstream_gene_variant ; 50.0bp to feature; MODIFIER silent_mutation Average:99.22; most accessible tissue: Callus, score: 99.802 N N N N
vg1125153506 G -> A LOC_Os11g41830.1 downstream_gene_variant ; 293.0bp to feature; MODIFIER silent_mutation Average:99.22; most accessible tissue: Callus, score: 99.802 N N N N
vg1125153506 G -> A LOC_Os11g41820-LOC_Os11g41830 intergenic_region ; MODIFIER silent_mutation Average:99.22; most accessible tissue: Callus, score: 99.802 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)
vg1125153506 G A -0.15 -0.33 -0.19 -0.19 -0.15 -0.15

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125153506 5.88E-13 1.95E-10 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
vg1125153506 7.64E-09 2.84E-10 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
vg1125153506 NA 1.25E-06 mr1398 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
vg1125153506 NA 4.17E-08 mr1551 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
vg1125153506 NA 9.27E-17 mr1593 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
vg1125153506 5.94E-14 1.64E-11 mr1644 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
vg1125153506 2.42E-11 2.10E-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
vg1125153506 NA 1.69E-08 mr1723 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
vg1125153506 1.43E-14 1.11E-13 mr1191_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
vg1125153506 5.34E-10 1.06E-14 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
vg1125153506 NA 1.82E-06 mr1250_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
vg1125153506 NA 2.13E-06 mr1295_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
vg1125153506 NA 1.49E-06 mr1423_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
vg1125153506 NA 1.89E-14 mr1539_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
vg1125153506 NA 3.87E-21 mr1593_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
vg1125153506 NA 3.36E-07 mr1723_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
vg1125153506 NA 7.26E-14 mr1732_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
vg1125153506 NA 7.87E-08 mr1733_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
vg1125153506 NA 9.71E-10 mr1769_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