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Detailed information for vg0614117993:

Variant ID: vg0614117993 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 14117993
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCCGGCCGATTCCACCCTCCGCGGCCACGATCTCACCGCCCCGCGACAATAAAAACGATCCCCGTGCTCTCCTCTCCCATTTTCCCAATTTTCCCGAGC[T/A]
CCCCGCGCCCTCTCCCGCTCTCCCCTCGCCAAGCTGAGCCGCCGCCGCCCGCCGGAGCTCTCCAGCCGCGCGCCGTTGCTGCTTCCGTCGCCCCCGCACT

Reverse complement sequence

AGTGCGGGGGCGACGGAAGCAGCAACGGCGCGCGGCTGGAGAGCTCCGGCGGGCGGCGGCGGCTCAGCTTGGCGAGGGGAGAGCGGGAGAGGGCGCGGGG[A/T]
GCTCGGGAAAATTGGGAAAATGGGAGAGGAGAGCACGGGGATCGTTTTTATTGTCGCGGGGCGGTGAGATCGTGGCCGCGGAGGGTGGAATCGGCCGGCA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.80% 2.20% 2.03% 0.00% NA
All Indica  2759 99.70% 0.00% 0.25% 0.00% NA
All Japonica  1512 87.40% 6.70% 5.82% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 99.60% 0.00% 0.43% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.00% 0.38% 0.00% NA
Temperate Japonica  767 82.40% 8.30% 9.26% 0.00% NA
Tropical Japonica  504 98.00% 0.20% 1.79% 0.00% NA
Japonica Intermediate  241 81.30% 15.40% 3.32% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 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
vg0614117993 T -> A LOC_Os06g24120.1 upstream_gene_variant ; 4854.0bp to feature; MODIFIER silent_mutation Average:89.068; most accessible tissue: Zhenshan97 flag leaf, score: 98.911 N N N N
vg0614117993 T -> A LOC_Os06g24130.1 intron_variant ; MODIFIER silent_mutation Average:89.068; most accessible tissue: Zhenshan97 flag leaf, score: 98.911 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)
vg0614117993 T A -0.02 -0.02 -0.02 -0.03 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0614117993 NA 1.07E-07 mr1071 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
vg0614117993 NA 8.14E-07 mr1140 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
vg0614117993 NA 7.70E-07 mr1203 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
vg0614117993 NA 9.73E-07 mr1395 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
vg0614117993 NA 6.31E-08 mr1613 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
vg0614117993 NA 4.19E-06 mr1618 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
vg0614117993 NA 3.05E-08 mr1913 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
vg0614117993 NA 8.12E-07 mr1071_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
vg0614117993 9.49E-07 9.75E-08 mr1100_2 Jap_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
vg0614117993 8.43E-06 1.21E-06 mr1203_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
vg0614117993 2.43E-06 2.17E-08 mr1613_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
vg0614117993 NA 5.04E-06 mr1619_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
vg0614117993 NA 8.43E-06 mr1795_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
vg0614117993 2.23E-06 1.86E-09 mr1913_2 Jap_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