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Detailed information for vg0916269577:

Variant ID: vg0916269577 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 16269577
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTGTGCTCAGTGATGATCTGTCTGCCTCTGCTCACCACTGGCATGAAGGTGTGGGTGTAAAGTTTATAAAGTATACGGATACACATTTGAAGTATTAAAC[G/A]
TAGATTAATACACAACAAATTACAGATTCCGTCTGTAAACTGTGAGACGAATTTATTAAGCATAATTAATCCGTCATTAGCAAATATTTACTGTAGCATC

Reverse complement sequence

GATGCTACAGTAAATATTTGCTAATGACGGATTAATTATGCTTAATAAATTCGTCTCACAGTTTACAGACGGAATCTGTAATTTGTTGTGTATTAATCTA[C/T]
GTTTAATACTTCAAATGTGTATCCGTATACTTTATAAACTTTACACCCACACCTTCATGCCAGTGGTGAGCAGAGGCAGACAGATCATCACTGAGCACAC

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 91.80% 7.80% 0.28% 0.15% NA
All Indica  2759 86.40% 13.20% 0.11% 0.25% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 96.30% 0.00% 3.72% 0.00% NA
Indica I  595 61.30% 38.30% 0.17% 0.17% NA
Indica II  465 97.80% 1.90% 0.00% 0.22% NA
Indica III  913 95.70% 3.90% 0.22% 0.11% NA
Indica Intermediate  786 87.90% 11.60% 0.00% 0.51% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0916269577 G -> DEL N N silent_mutation Average:83.797; most accessible tissue: Zhenshan97 flower, score: 95.104 N N N N
vg0916269577 G -> A LOC_Os09g26770.2 downstream_gene_variant ; 3703.0bp to feature; MODIFIER silent_mutation Average:83.797; most accessible tissue: Zhenshan97 flower, score: 95.104 N N N N
vg0916269577 G -> A LOC_Os09g26780.1 downstream_gene_variant ; 3759.0bp to feature; MODIFIER silent_mutation Average:83.797; most accessible tissue: Zhenshan97 flower, score: 95.104 N N N N
vg0916269577 G -> A LOC_Os09g26770.3 downstream_gene_variant ; 3663.0bp to feature; MODIFIER silent_mutation Average:83.797; most accessible tissue: Zhenshan97 flower, score: 95.104 N N N N
vg0916269577 G -> A LOC_Os09g26770-LOC_Os09g26780 intergenic_region ; MODIFIER silent_mutation Average:83.797; most accessible tissue: Zhenshan97 flower, score: 95.104 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)
vg0916269577 G A 0.09 0.06 0.05 0.01 0.04 0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0916269577 NA 5.18E-06 mr1136 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
vg0916269577 NA 7.10E-09 mr1138 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
vg0916269577 1.78E-07 1.19E-19 mr1707 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
vg0916269577 9.85E-06 5.07E-12 mr1707 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
vg0916269577 1.13E-07 3.21E-22 mr1728 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
vg0916269577 3.17E-06 7.10E-15 mr1728 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
vg0916269577 1.55E-07 1.37E-19 mr1860 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
vg0916269577 4.60E-07 7.96E-14 mr1860 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
vg0916269577 NA 4.44E-07 mr1136_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
vg0916269577 9.23E-06 NA mr1138_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
vg0916269577 NA 5.97E-09 mr1138_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
vg0916269577 NA 9.46E-06 mr1349_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
vg0916269577 NA 4.51E-07 mr1355_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
vg0916269577 NA 4.17E-06 mr1360_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
vg0916269577 NA 9.18E-06 mr1457_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
vg0916269577 NA 3.09E-10 mr1458_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
vg0916269577 1.29E-06 9.19E-17 mr1707_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
vg0916269577 NA 6.47E-10 mr1707_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
vg0916269577 9.87E-07 1.77E-24 mr1728_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
vg0916269577 NA 5.84E-14 mr1728_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
vg0916269577 3.73E-06 6.54E-19 mr1860_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
vg0916269577 8.05E-06 3.54E-13 mr1860_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
vg0916269577 NA 4.40E-11 mr1895_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
vg0916269577 NA 1.67E-09 mr1895_2 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
vg0916269577 NA 3.32E-06 mr1899_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
vg0916269577 NA 1.41E-06 mr1928_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
vg0916269577 NA 2.23E-07 mr1928_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
vg0916269577 NA 2.81E-06 mr1931_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
vg0916269577 NA 3.65E-07 mr1931_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