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Detailed information for vg0135141098:

Variant ID: vg0135141098 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35141098
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCGCGCGTGCGTGCGGGGTGACGTACGCGCGGTGCGGTGCGGGCTCCATCCAACCACCCGCCGCGCGACGCAGGGCAGGTTTTCGCCGGAGAGAGCGAC[G/T]
CGGGATGGATGGATGAGTAGGCGGGGGGGCGTGCACGGCGCCATCGGTTCGGTTGGGCCGGGCGCTATCGAGCCAATAATGAACGGAACGGTCCGAACTG

Reverse complement sequence

CAGTTCGGACCGTTCCGTTCATTATTGGCTCGATAGCGCCCGGCCCAACCGAACCGATGGCGCCGTGCACGCCCCCCCGCCTACTCATCCATCCATCCCG[C/A]
GTCGCTCTCTCCGGCGAAAACCTGCCCTGCGTCGCGCGGCGGGTGGTTGGATGGAGCCCGCACCGCACCGCGCGTACGTCACCCCGCACGCACGCGCGCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.70% 12.30% 0.00% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 68.80% 31.20% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 97.70% 2.30% 0.00% 0.00% NA
Tropical Japonica  504 28.00% 72.00% 0.00% 0.00% NA
Japonica Intermediate  241 62.70% 37.30% 0.00% 0.00% NA
VI/Aromatic  96 14.60% 85.40% 0.00% 0.00% NA
Intermediate  90 76.70% 23.30% 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
vg0135141098 G -> T LOC_Os01g60760.1 upstream_gene_variant ; 1565.0bp to feature; MODIFIER silent_mutation Average:97.361; most accessible tissue: Zhenshan97 flower, score: 99.577 N N N N
vg0135141098 G -> T LOC_Os01g60770.1 upstream_gene_variant ; 4418.0bp to feature; MODIFIER silent_mutation Average:97.361; most accessible tissue: Zhenshan97 flower, score: 99.577 N N N N
vg0135141098 G -> T LOC_Os01g60760-LOC_Os01g60770 intergenic_region ; MODIFIER silent_mutation Average:97.361; most accessible tissue: Zhenshan97 flower, score: 99.577 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)
vg0135141098 G T -0.09 -0.18 -0.12 0.01 -0.08 -0.1

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0135141098 NA 1.55E-09 mr1097 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
vg0135141098 NA 4.31E-10 mr1128 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
vg0135141098 NA 6.31E-07 mr1229 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
vg0135141098 1.88E-06 NA mr1517 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
vg0135141098 NA 4.18E-08 mr1993 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
vg0135141098 NA 1.71E-11 mr1593_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
vg0135141098 NA 2.36E-10 mr1784_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
vg0135141098 NA 1.31E-09 mr1862_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