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Detailed information for vg1120950747:

Variant ID: vg1120950747 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 20950747
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.51, T: 0.47, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


GAGCGGCGCACTGCCGCCGCTGACCGAGATGGTGTACAGCGAGGTGGCTAGGGATGCAAGTGGATAGTCTCGCTACCCGCATAAAACCCGCTTGCTAGTT[C/T]
AATTTTCACATGGTAGTAAAAAAACTTAAAGAAAAAATAAACCAGAAGTGAGATAAGCGGGCTAAAAAAACCGCTTATCCGCCCCGCTTACATCCCTAGA

Reverse complement sequence

TCTAGGGATGTAAGCGGGGCGGATAAGCGGTTTTTTTAGCCCGCTTATCTCACTTCTGGTTTATTTTTTCTTTAAGTTTTTTTACTACCATGTGAAAATT[G/A]
AACTAGCAAGCGGGTTTTATGCGGGTAGCGAGACTATCCACTTGCATCCCTAGCCACCTCGCTGTACACCATCTCGGTCAGCGGCGGCAGTGCGCCGCTC

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 55.20% 43.30% 0.17% 1.29% NA
All Indica  2759 32.80% 65.80% 0.22% 1.23% NA
All Japonica  1512 96.40% 2.20% 0.00% 1.46% NA
Aus  269 35.70% 62.80% 0.37% 1.12% NA
Indica I  595 62.70% 37.00% 0.34% 0.00% NA
Indica II  465 29.20% 68.00% 0.22% 2.58% NA
Indica III  913 13.10% 85.70% 0.22% 0.99% NA
Indica Intermediate  786 35.00% 63.20% 0.13% 1.65% NA
Temperate Japonica  767 98.30% 1.60% 0.00% 0.13% NA
Tropical Japonica  504 93.10% 2.80% 0.00% 4.17% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 66.70% 30.00% 1.11% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1120950747 C -> T LOC_Os11g35710.1 intron_variant ; MODIFIER silent_mutation Average:82.895; most accessible tissue: Zhenshan97 panicle, score: 87.451 N N N N
vg1120950747 C -> DEL N N silent_mutation Average:82.895; most accessible tissue: Zhenshan97 panicle, score: 87.451 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)
vg1120950747 C T 0.05 0.03 0.02 0.05 0.06 0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1120950747 NA 1.61E-06 mr1013 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
vg1120950747 NA 5.78E-07 mr1034 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
vg1120950747 NA 9.75E-06 mr1745 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
vg1120950747 2.43E-06 2.42E-06 mr1966 Ind_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