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Detailed information for vg0501509057:

Variant ID: vg0501509057 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 1509057
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.10, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


GGACGCCATTAACAGCGAGCCCACGCGCGATCGGGAATATCGGGCTGCTCCACCCGCAGCGACGCGCCGATCTGACGCTAAACCAGACATTAAGGAGGAG[G/A]
AGGAGGGGGGGGAGATCGGGATCGGGGATGGAGACGATGAGATGCAAGAGAATTCGAGGGGAGGAAGGAGAGGGTTGGTTGGGTTGGACGGATTGGGGGT

Reverse complement sequence

ACCCCCAATCCGTCCAACCCAACCAACCCTCTCCTTCCTCCCCTCGAATTCTCTTGCATCTCATCGTCTCCATCCCCGATCCCGATCTCCCCCCCCTCCT[C/T]
CTCCTCCTTAATGTCTGGTTTAGCGTCAGATCGGCGCGTCGCTGCGGGTGGAGCAGCCCGATATTCCCGATCGCGCGTGGGCTCGCTGTTAATGGCGTCC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.50% 44.80% 0.42% 0.25% NA
All Indica  2759 80.20% 19.80% 0.00% 0.00% NA
All Japonica  1512 3.70% 94.30% 1.26% 0.73% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 95.50% 4.50% 0.00% 0.00% NA
Indica II  465 63.40% 36.60% 0.00% 0.00% NA
Indica III  913 78.60% 21.40% 0.00% 0.00% NA
Indica Intermediate  786 80.30% 19.70% 0.00% 0.00% NA
Temperate Japonica  767 3.00% 95.60% 1.04% 0.39% NA
Tropical Japonica  504 5.00% 94.80% 0.20% 0.00% NA
Japonica Intermediate  241 3.30% 89.20% 4.15% 3.32% NA
VI/Aromatic  96 12.50% 86.50% 1.04% 0.00% NA
Intermediate  90 35.60% 63.30% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0501509057 G -> DEL N N silent_mutation Average:81.84; most accessible tissue: Zhenshan97 flower, score: 99.507 N N N N
vg0501509057 G -> A LOC_Os05g03550.1 upstream_gene_variant ; 1218.0bp to feature; MODIFIER silent_mutation Average:81.84; most accessible tissue: Zhenshan97 flower, score: 99.507 N N N N
vg0501509057 G -> A LOC_Os05g03560.1 upstream_gene_variant ; 1992.0bp to feature; MODIFIER silent_mutation Average:81.84; most accessible tissue: Zhenshan97 flower, score: 99.507 N N N N
vg0501509057 G -> A LOC_Os05g03550-LOC_Os05g03560 intergenic_region ; MODIFIER silent_mutation Average:81.84; most accessible tissue: Zhenshan97 flower, score: 99.507 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)
vg0501509057 G A -0.02 -0.03 -0.03 -0.02 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0501509057 NA 2.86E-06 mr1028 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
vg0501509057 NA 7.96E-23 mr1150 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
vg0501509057 NA 2.65E-06 mr1170 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
vg0501509057 NA 1.88E-10 mr1275 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
vg0501509057 NA 4.54E-09 mr1302 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
vg0501509057 NA 2.44E-11 mr1307 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
vg0501509057 NA 2.08E-06 mr1392 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
vg0501509057 NA 3.61E-06 mr1397 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
vg0501509057 NA 9.12E-07 mr1420 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
vg0501509057 NA 6.93E-08 mr1453 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
vg0501509057 3.85E-06 3.83E-06 mr1497 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
vg0501509057 6.51E-06 6.51E-06 mr1497 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
vg0501509057 NA 4.63E-06 mr1500 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
vg0501509057 NA 2.77E-08 mr1514 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
vg0501509057 NA 4.14E-06 mr1626 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
vg0501509057 NA 7.84E-06 mr1631 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
vg0501509057 NA 4.24E-06 mr1679 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
vg0501509057 NA 1.69E-06 mr1681 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
vg0501509057 NA 8.88E-06 mr1720 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
vg0501509057 NA 4.46E-07 mr1764 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
vg0501509057 NA 5.59E-06 mr1772 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
vg0501509057 NA 1.51E-08 mr1776 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
vg0501509057 NA 8.07E-06 mr1802 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
vg0501509057 NA 2.33E-09 mr1986 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
vg0501509057 NA 7.30E-13 mr1191_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
vg0501509057 NA 1.07E-09 mr1660_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
vg0501509057 NA 1.06E-13 mr1904_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
vg0501509057 NA 2.38E-06 mr1977_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