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Detailed information for vg0227957829:

Variant ID: vg0227957829 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 27957829
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGTTGGTTTGGGAGATGCAACGGTTGGCGGACGAGGAATTCGGGACGTTGGGCTTAAGGCTACAATGGGCAACAAAAATTAGGAATAATTTCACCGGAG[G/A]
TCCCTCAACTTAACAATGAGATTTTTTTAACATCCCTTTAACCATAAAAGCAGAAATGTCTACCCCTAAACTCACTCAAACCGTTCAAAGAAGGTCCCAT

Reverse complement sequence

ATGGGACCTTCTTTGAACGGTTTGAGTGAGTTTAGGGGTAGACATTTCTGCTTTTATGGTTAAAGGGATGTTAAAAAAATCTCATTGTTAAGTTGAGGGA[C/T]
CTCCGGTGAAATTATTCCTAATTTTTGTTGCCCATTGTAGCCTTAAGCCCAACGTCCCGAATTCCTCGTCCGCCAACCGTTGCATCTCCCAAACCAACGA

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 91.50% 8.50% 0.00% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 87.40% 12.60% 0.00% 0.00% NA
Aus  269 58.70% 41.30% 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 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 63.90% 36.10% 0.00% 0.00% NA
Japonica Intermediate  241 96.70% 3.30% 0.00% 0.00% NA
VI/Aromatic  96 20.80% 79.20% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg0227957829 G -> A LOC_Os02g45860.1 upstream_gene_variant ; 1968.0bp to feature; MODIFIER silent_mutation Average:85.847; most accessible tissue: Zhenshan97 root, score: 94.906 N N N N
vg0227957829 G -> A LOC_Os02g45870.1 upstream_gene_variant ; 4277.0bp to feature; MODIFIER silent_mutation Average:85.847; most accessible tissue: Zhenshan97 root, score: 94.906 N N N N
vg0227957829 G -> A LOC_Os02g45850-LOC_Os02g45860 intergenic_region ; MODIFIER silent_mutation Average:85.847; most accessible tissue: Zhenshan97 root, score: 94.906 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)
vg0227957829 G A -0.47 -0.4 -0.32 -0.34 -0.39 -0.42

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0227957829 NA 1.78E-06 mr1250_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
vg0227957829 NA 6.16E-06 mr1295_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
vg0227957829 NA 4.15E-06 mr1341_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
vg0227957829 4.10E-06 NA mr1410_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
vg0227957829 NA 2.37E-06 mr1715_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
vg0227957829 1.16E-06 NA mr1733_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
vg0227957829 8.71E-07 NA mr1993_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