Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0216182780:

Variant ID: vg0216182780 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 16182780
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATTTAAAACTTTCAACTCAAGATTTTTTAAATTTTCAACTCCGATTTAAAAATTTTTAAGTCAAGATTTAAAAACTTTCAACTCGGATTTGAAAACTTT[C/T]
AATTCAAACTTGAAAACGTTCAACTCGGATTTGAAAACTTTCAATTCAGACTTGAAAACTTTCAACTGAAGATTTGAAACTTTCAACTCAAATTTGAAAA

Reverse complement sequence

TTTTCAAATTTGAGTTGAAAGTTTCAAATCTTCAGTTGAAAGTTTTCAAGTCTGAATTGAAAGTTTTCAAATCCGAGTTGAACGTTTTCAAGTTTGAATT[G/A]
AAAGTTTTCAAATCCGAGTTGAAAGTTTTTAAATCTTGACTTAAAAATTTTTAAATCGGAGTTGAAAATTTAAAAAATCTTGAGTTGAAAGTTTTAAATC

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 95.40% 0.80% 3.79% 0.00% NA
All Indica  2759 94.30% 1.10% 4.68% 0.00% NA
All Japonica  1512 99.70% 0.00% 0.26% 0.00% NA
Aus  269 80.70% 3.00% 16.36% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 85.60% 1.90% 12.47% 0.00% NA
Indica III  913 95.20% 1.10% 3.72% 0.00% NA
Indica Intermediate  786 94.00% 1.30% 4.71% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 98.80% 0.00% 1.24% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 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
vg0216182780 C -> T LOC_Os02g27440.2 downstream_gene_variant ; 2443.0bp to feature; MODIFIER silent_mutation Average:51.87; most accessible tissue: Callus, score: 87.142 N N N N
vg0216182780 C -> T LOC_Os02g27450.1 downstream_gene_variant ; 821.0bp to feature; MODIFIER silent_mutation Average:51.87; most accessible tissue: Callus, score: 87.142 N N N N
vg0216182780 C -> T LOC_Os02g27440.3 downstream_gene_variant ; 2443.0bp to feature; MODIFIER silent_mutation Average:51.87; most accessible tissue: Callus, score: 87.142 N N N N
vg0216182780 C -> T LOC_Os02g27440.4 downstream_gene_variant ; 2443.0bp to feature; MODIFIER silent_mutation Average:51.87; most accessible tissue: Callus, score: 87.142 N N N N
vg0216182780 C -> T LOC_Os02g27440-LOC_Os02g27450 intergenic_region ; MODIFIER silent_mutation Average:51.87; most accessible tissue: Callus, score: 87.142 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)
vg0216182780 C T 0.01 0.0 0.0 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0216182780 NA 1.49E-06 mr1129 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
vg0216182780 4.78E-06 7.11E-13 mr1317 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
vg0216182780 8.30E-08 9.93E-14 mr1317 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
vg0216182780 NA 3.96E-06 mr1818 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
vg0216182780 NA 1.34E-25 mr1855 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
vg0216182780 NA 1.03E-17 mr1855 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
vg0216182780 NA 7.23E-07 mr1914 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
vg0216182780 NA 3.04E-12 mr1317_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
vg0216182780 2.32E-06 2.14E-13 mr1317_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
vg0216182780 NA 1.40E-06 mr1608_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
vg0216182780 NA 5.86E-07 mr1610_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
vg0216182780 NA 1.65E-06 mr1818_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
vg0216182780 1.32E-07 8.71E-26 mr1855_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
vg0216182780 9.45E-09 2.58E-17 mr1855_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
vg0216182780 NA 3.13E-06 mr1896_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
vg0216182780 NA 9.86E-09 mr1897_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
vg0216182780 NA 1.05E-13 mr1914_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
vg0216182780 2.88E-06 6.46E-13 mr1914_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
vg0216182780 NA 1.82E-08 mr1927_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