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Detailed information for vg0800158999:

Variant ID: vg0800158999 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 158999
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATGAAATTAGTTTTTTCATTCGTGTCCGAAAAATCCTTCCGATATCCGGTCAAACGTCCGATGTGACACCCAAAATTTTTCATTTCTCGCGAACTAAAC[G/A,T]
GGGCCTTAGGTCCGTGCATTGCAGCCACAGACGTGCATATCACCTCGTCCGACCCGGCTTTAACATAGCTAGCGAGTACTACCTTTATTTATTTACAACT

Reverse complement sequence

AGTTGTAAATAAATAAAGGTAGTACTCGCTAGCTATGTTAAAGCCGGGTCGGACGAGGTGATATGCACGTCTGTGGCTGCAATGCACGGACCTAAGGCCC[C/T,A]
GTTTAGTTCGCGAGAAATGAAAAATTTTGGGTGTCACATCGGACGTTTGACCGGATATCGGAAGGATTTTTCGGACACGAATGAAAAAACTAATTTCATA

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 59.40% 0.90% 1.84% 37.83% T: 0.02%
All Indica  2759 48.10% 0.00% 1.92% 49.98% NA
All Japonica  1512 83.60% 2.80% 1.65% 11.90% NA
Aus  269 52.80% 0.00% 2.60% 44.24% T: 0.37%
Indica I  595 68.20% 0.00% 1.18% 30.59% NA
Indica II  465 25.80% 0.00% 2.37% 71.83% NA
Indica III  913 46.00% 0.00% 1.97% 52.03% NA
Indica Intermediate  786 48.50% 0.00% 2.16% 49.36% NA
Temperate Japonica  767 90.50% 4.40% 2.48% 2.61% NA
Tropical Japonica  504 72.20% 0.40% 0.79% 26.59% NA
Japonica Intermediate  241 85.50% 2.90% 0.83% 10.79% NA
VI/Aromatic  96 20.80% 0.00% 2.08% 77.08% NA
Intermediate  90 60.00% 0.00% 0.00% 40.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0800158999 G -> T LOC_Os08g01230.1 upstream_gene_variant ; 2419.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0800158999 G -> T LOC_Os08g01240.1 upstream_gene_variant ; 116.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0800158999 G -> T LOC_Os08g01230-LOC_Os08g01240 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0800158999 G -> A LOC_Os08g01230.1 upstream_gene_variant ; 2419.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0800158999 G -> A LOC_Os08g01240.1 upstream_gene_variant ; 116.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0800158999 G -> A LOC_Os08g01230-LOC_Os08g01240 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0800158999 G -> DEL N N silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 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)
vg0800158999 G A -0.02 -0.06 -0.07 -0.01 -0.05 -0.03
vg0800158999 G T -0.1 -0.07 -0.05 -0.05 -0.07 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0800158999 NA 4.47E-07 mr1045 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
vg0800158999 NA 8.83E-06 mr1318 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
vg0800158999 1.78E-06 1.78E-06 mr1881 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