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Detailed information for vg0327447631:

Variant ID: vg0327447631 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 27447631
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTAATATGAAAGTTACTTAAAAAATCAAATTAATCATTTTTTTAAAAAATAACTAATACTTAATTAATCGCGCGCTAATAAACGGTTCCGTTTTTCGT[G/A]
CAGAGGGGATGGTTTCCAACCCCAACAATCGAACACAGGCGCAAGCTAATCTGCTGCTGGAAATTGTGGACTCACACACATACACAAATGAACGAGAACT

Reverse complement sequence

AGTTCTCGTTCATTTGTGTATGTGTGTGAGTCCACAATTTCCAGCAGCAGATTAGCTTGCGCCTGTGTTCGATTGTTGGGGTTGGAAACCATCCCCTCTG[C/T]
ACGAAAAACGGAACCGTTTATTAGCGCGCGATTAATTAAGTATTAGTTATTTTTTAAAAAAATGATTAATTTGATTTTTTAAGTAACTTTCATATTAAAT

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 93.40% 5.50% 0.04% 1.04% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 83.10% 13.60% 0.13% 3.24% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 70.30% 25.70% 0.26% 3.78% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 88.40% 3.30% 0.00% 8.30% NA
VI/Aromatic  96 62.50% 37.50% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0327447631 G -> A LOC_Os03g48220.1 upstream_gene_variant ; 1858.0bp to feature; MODIFIER silent_mutation Average:83.364; most accessible tissue: Zhenshan97 flower, score: 96.791 N N N N
vg0327447631 G -> A LOC_Os03g48225.1 downstream_gene_variant ; 41.0bp to feature; MODIFIER silent_mutation Average:83.364; most accessible tissue: Zhenshan97 flower, score: 96.791 N N N N
vg0327447631 G -> A LOC_Os03g48230.1 downstream_gene_variant ; 1178.0bp to feature; MODIFIER silent_mutation Average:83.364; most accessible tissue: Zhenshan97 flower, score: 96.791 N N N N
vg0327447631 G -> A LOC_Os03g48235.1 downstream_gene_variant ; 2587.0bp to feature; MODIFIER silent_mutation Average:83.364; most accessible tissue: Zhenshan97 flower, score: 96.791 N N N N
vg0327447631 G -> A LOC_Os03g48220-LOC_Os03g48225 intergenic_region ; MODIFIER silent_mutation Average:83.364; most accessible tissue: Zhenshan97 flower, score: 96.791 N N N N
vg0327447631 G -> DEL N N silent_mutation Average:83.364; most accessible tissue: Zhenshan97 flower, score: 96.791 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)
vg0327447631 G A -0.01 0.0 0.0 0.03 0.02 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0327447631 1.41E-07 NA mr1166 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
vg0327447631 1.77E-14 NA mr1210 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
vg0327447631 1.17E-08 3.33E-12 mr1210 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
vg0327447631 3.34E-14 NA mr1305 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
vg0327447631 3.35E-09 2.02E-12 mr1305 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
vg0327447631 1.05E-07 1.14E-09 mr1379 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
vg0327447631 1.27E-07 NA mr1409 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
vg0327447631 7.48E-07 NA mr1515 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
vg0327447631 3.30E-07 NA mr1559 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
vg0327447631 4.88E-10 5.40E-11 mr1585 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
vg0327447631 1.42E-06 1.17E-11 mr1585 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
vg0327447631 1.98E-18 NA mr1586 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
vg0327447631 3.22E-09 9.75E-13 mr1586 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
vg0327447631 3.83E-07 NA mr1649 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
vg0327447631 3.01E-11 NA mr1765 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
vg0327447631 6.28E-07 6.58E-11 mr1765 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
vg0327447631 1.61E-07 NA mr1305_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
vg0327447631 NA 1.38E-07 mr1305_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
vg0327447631 3.82E-08 2.40E-09 mr1585_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
vg0327447631 6.40E-06 3.46E-09 mr1585_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