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Detailed information for vg0413771259:

Variant ID: vg0413771259 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 13771259
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


AACACCTCCAAGGAGGAAACAGCACCCGCATACATCGATGTCACCGATCCTGTAAGACCAGACAAGGATTTCACCCAAGACTGTCGCCGATCCTGTAAGA[C/T]
CAGGCAAGAATTTCACCTAAGACTACCTTAAAACGTGTAGAACCTTCAAGAAACAAGAGCAAAAGTGTTGAGTGTTATCGTTGCCCAACTCATCGGCTGA

Reverse complement sequence

TCAGCCGATGAGTTGGGCAACGATAACACTCAACACTTTTGCTCTTGTTTCTTGAAGGTTCTACACGTTTTAAGGTAGTCTTAGGTGAAATTCTTGCCTG[G/A]
TCTTACAGGATCGGCGACAGTCTTGGGTGAAATCCTTGTCTGGTCTTACAGGATCGGTGACATCGATGTATGCGGGTGCTGTTTCCTCCTTGGAGGTGTT

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 73.30% 26.60% 0.11% 0.00% NA
All Indica  2759 62.80% 37.00% 0.18% 0.00% NA
All Japonica  1512 90.90% 9.10% 0.00% 0.00% NA
Aus  269 92.60% 7.40% 0.00% 0.00% NA
Indica I  595 59.50% 40.30% 0.17% 0.00% NA
Indica II  465 74.40% 25.60% 0.00% 0.00% NA
Indica III  913 51.40% 48.40% 0.22% 0.00% NA
Indica Intermediate  786 71.80% 28.00% 0.25% 0.00% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 85.70% 14.30% 0.00% 0.00% NA
Japonica Intermediate  241 78.40% 21.60% 0.00% 0.00% NA
VI/Aromatic  96 45.80% 54.20% 0.00% 0.00% NA
Intermediate  90 68.90% 31.10% 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
vg0413771259 C -> T LOC_Os04g24100.1 upstream_gene_variant ; 4724.0bp to feature; MODIFIER silent_mutation Average:81.045; most accessible tissue: Zhenshan97 flower, score: 91.937 N N N N
vg0413771259 C -> T LOC_Os04g24110.1 upstream_gene_variant ; 62.0bp to feature; MODIFIER silent_mutation Average:81.045; most accessible tissue: Zhenshan97 flower, score: 91.937 N N N N
vg0413771259 C -> T LOC_Os04g24100-LOC_Os04g24110 intergenic_region ; MODIFIER silent_mutation Average:81.045; most accessible tissue: Zhenshan97 flower, score: 91.937 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)
vg0413771259 C T -0.05 -0.07 -0.06 -0.03 -0.03 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0413771259 5.96E-06 NA mr1584 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
vg0413771259 4.58E-06 NA mr1730 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
vg0413771259 8.93E-06 NA mr1350_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
vg0413771259 3.22E-08 3.69E-11 mr1350_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
vg0413771259 1.59E-07 1.92E-08 mr1730_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