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Detailed information for vg1125603928:

Variant ID: vg1125603928 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25603928
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.67, T: 0.33, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


GCATGGTGTAATCCCATCTTCCCAATTAACAGACGTAACAGACAATGTTTACCAGATAGCGTGCCTTGTTTGATTTTTCGTTCTTTACTACGGTAATACA[C/T]
AGCAAGGATTGAAATTGACGTGCGTATTCGTCTTGAGCAATAGATTTAACGAGTTAACCAACAAAAATGGAGATGTTAGTTGCGAACAGGCCACGAAACA

Reverse complement sequence

TGTTTCGTGGCCTGTTCGCAACTAACATCTCCATTTTTGTTGGTTAACTCGTTAAATCTATTGCTCAAGACGAATACGCACGTCAATTTCAATCCTTGCT[G/A]
TGTATTACCGTAGTAAAGAACGAAAAATCAAACAAGGCACGCTATCTGGTAAACATTGTCTGTTACGTCTGTTAATTGGGAAGATGGGATTACACCATGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.90% 42.00% 0.17% 0.00% NA
All Indica  2759 39.70% 60.00% 0.25% 0.00% NA
All Japonica  1512 91.70% 8.30% 0.00% 0.00% NA
Aus  269 60.60% 39.00% 0.37% 0.00% NA
Indica I  595 52.40% 47.20% 0.34% 0.00% NA
Indica II  465 27.10% 72.70% 0.22% 0.00% NA
Indica III  913 42.80% 56.80% 0.33% 0.00% NA
Indica Intermediate  786 34.00% 65.90% 0.13% 0.00% NA
Temperate Japonica  767 95.30% 4.70% 0.00% 0.00% NA
Tropical Japonica  504 85.50% 14.50% 0.00% 0.00% NA
Japonica Intermediate  241 92.90% 7.10% 0.00% 0.00% NA
VI/Aromatic  96 44.80% 55.20% 0.00% 0.00% NA
Intermediate  90 52.20% 47.80% 0.00% 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
vg1125603928 C -> T LOC_Os11g42510.1 upstream_gene_variant ; 1510.0bp to feature; MODIFIER silent_mutation Average:64.724; most accessible tissue: Callus, score: 82.449 N N N N
vg1125603928 C -> T LOC_Os11g42520.1 upstream_gene_variant ; 4480.0bp to feature; MODIFIER silent_mutation Average:64.724; most accessible tissue: Callus, score: 82.449 N N N N
vg1125603928 C -> T LOC_Os11g42510.2 upstream_gene_variant ; 439.0bp to feature; MODIFIER silent_mutation Average:64.724; most accessible tissue: Callus, score: 82.449 N N N N
vg1125603928 C -> T LOC_Os11g42510-LOC_Os11g42520 intergenic_region ; MODIFIER silent_mutation Average:64.724; most accessible tissue: Callus, score: 82.449 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)
vg1125603928 C T -0.09 -0.02 -0.03 -0.02 -0.03 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125603928 2.92E-15 2.35E-19 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
vg1125603928 6.27E-09 2.23E-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
vg1125603928 2.22E-06 2.22E-06 mr1191 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
vg1125603928 2.50E-06 NA mr1238 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
vg1125603928 7.81E-06 NA mr1238 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
vg1125603928 6.26E-06 NA mr1309 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
vg1125603928 1.97E-20 7.47E-24 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
vg1125603928 1.10E-12 3.17E-10 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
vg1125603928 5.15E-09 5.14E-09 mr1644 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
vg1125603928 NA 5.84E-06 mr1743 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
vg1125603928 1.10E-06 NA mr1841 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
vg1125603928 7.77E-07 NA mr1900 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
vg1125603928 1.31E-06 6.06E-12 mr1945 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
vg1125603928 2.56E-20 3.95E-24 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
vg1125603928 8.81E-14 1.15E-09 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
vg1125603928 1.09E-06 1.09E-06 mr1191_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
vg1125603928 9.98E-06 NA mr1900_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