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Detailed information for vg0805947083:

Variant ID: vg0805947083 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 5947083
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTACTGTTTAGTTAAATGCTGTCCAAGAATTGTTTACCACTTTGGGTTTTGATGAATTTTCTTATCAGGCTAGTATGGAGGAGTCTGATAATCAGGGTCT[G/A]
ATGGCAATCTCAGTTCAGGCAGTGCATGGATCTGAAGCTGTGGGTTATATGAGAATGTTAGGATTCATTCAAGGCAAAGAGTTTTGATTTTGGTGGATTC

Reverse complement sequence

GAATCCACCAAAATCAAAACTCTTTGCCTTGAATGAATCCTAACATTCTCATATAACCCACAGCTTCAGATCCATGCACTGCCTGAACTGAGATTGCCAT[C/T]
AGACCCTGATTATCAGACTCCTCCATACTAGCCTGATAAGAAAATTCATCAAAACCCAAAGTGGTAAACAATTCTTGGACAGCATTTAACTAAACAGTAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 68.90% 4.80% 1.74% 24.61% NA
All Indica  2759 58.80% 8.10% 2.14% 30.99% NA
All Japonica  1512 94.80% 0.10% 0.33% 4.76% NA
Aus  269 43.90% 0.00% 4.83% 51.30% NA
Indica I  595 35.80% 3.40% 5.71% 55.13% NA
Indica II  465 89.50% 0.60% 0.86% 9.03% NA
Indica III  913 60.20% 11.80% 0.77% 27.16% NA
Indica Intermediate  786 56.40% 11.70% 1.78% 30.15% NA
Temperate Japonica  767 98.40% 0.00% 0.39% 1.17% NA
Tropical Japonica  504 92.70% 0.20% 0.00% 7.14% NA
Japonica Intermediate  241 88.00% 0.00% 0.83% 11.20% NA
VI/Aromatic  96 21.90% 0.00% 5.21% 72.92% NA
Intermediate  90 67.80% 1.10% 0.00% 31.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0805947083 G -> A LOC_Os08g10244.1 5_prime_UTR_variant ; 647.0bp to feature; MODIFIER silent_mutation Average:45.69; most accessible tissue: Minghui63 young leaf, score: 91.842 N N N N
vg0805947083 G -> A LOC_Os08g10250.1 upstream_gene_variant ; 4081.0bp to feature; MODIFIER silent_mutation Average:45.69; most accessible tissue: Minghui63 young leaf, score: 91.842 N N N N
vg0805947083 G -> A LOC_Os08g10250 intragenic_variant ; MODIFIER silent_mutation Average:45.69; most accessible tissue: Minghui63 young leaf, score: 91.842 N N N N
vg0805947083 G -> DEL N N silent_mutation Average:45.69; most accessible tissue: Minghui63 young leaf, score: 91.842 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)
vg0805947083 G A -0.04 -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
vg0805947083 NA 2.58E-08 mr1068 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
vg0805947083 NA 1.98E-07 mr1078 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
vg0805947083 NA 2.97E-07 mr1096 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
vg0805947083 NA 1.56E-06 mr1121 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
vg0805947083 NA 5.63E-08 mr1155 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
vg0805947083 NA 5.68E-07 mr1200 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
vg0805947083 NA 6.25E-09 mr1068_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
vg0805947083 NA 6.17E-08 mr1078_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
vg0805947083 NA 2.46E-06 mr1090_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
vg0805947083 NA 2.83E-06 mr1096_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
vg0805947083 NA 4.51E-07 mr1121_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
vg0805947083 NA 1.73E-08 mr1155_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
vg0805947083 NA 3.48E-08 mr1200_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
vg0805947083 7.05E-06 NA mr1265_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
vg0805947083 5.73E-06 7.68E-06 mr1265_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
vg0805947083 2.28E-07 2.08E-07 mr1528_2 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
vg0805947083 6.70E-07 5.15E-08 mr1528_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