Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0820097251:

Variant ID: vg0820097251 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 20097251
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.64, A: 0.36, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


CTAGGCCGAGCAGCGACGCGGCGGCAGCACCACCACCGGTGGCGCCTCCACTGCCCTCAGCCGCCGCCGAGGCCGCCGCCCTCAGCCGCTGCCCCATCCT[A/G]
CCGCTGACCATGAGAGAGAGAGGAAGAATGAGGAGAGTGAGAGAGATAGAAGAGAGAGAGGAAGAGTGAAAGAGAGAGCGCGTATGACAGGTGGGTCCCA

Reverse complement sequence

TGGGACCCACCTGTCATACGCGCTCTCTCTTTCACTCTTCCTCTCTCTCTTCTATCTCTCTCACTCTCCTCATTCTTCCTCTCTCTCTCATGGTCAGCGG[T/C]
AGGATGGGGCAGCGGCTGAGGGCGGCGGCCTCGGCGGCGGCTGAGGGCAGTGGAGGCGCCACCGGTGGTGGTGCTGCCGCCGCGTCGCTGCTCGGCCTAG

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 66.50% 33.30% 0.19% 0.00% NA
All Indica  2759 60.50% 39.40% 0.14% 0.00% NA
All Japonica  1512 90.70% 9.20% 0.07% 0.00% NA
Aus  269 1.90% 97.80% 0.37% 0.00% NA
Indica I  595 52.30% 47.60% 0.17% 0.00% NA
Indica II  465 83.00% 17.00% 0.00% 0.00% NA
Indica III  913 51.60% 48.40% 0.00% 0.00% NA
Indica Intermediate  786 63.70% 35.90% 0.38% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 76.60% 23.20% 0.20% 0.00% NA
Japonica Intermediate  241 91.70% 8.30% 0.00% 0.00% NA
VI/Aromatic  96 41.70% 57.30% 1.04% 0.00% NA
Intermediate  90 62.20% 35.60% 2.22% 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
vg0820097251 A -> G LOC_Os08g32450.1 downstream_gene_variant ; 3223.0bp to feature; MODIFIER silent_mutation Average:84.917; most accessible tissue: Minghui63 panicle, score: 97.329 N N N N
vg0820097251 A -> G LOC_Os08g32460.1 downstream_gene_variant ; 286.0bp to feature; MODIFIER silent_mutation Average:84.917; most accessible tissue: Minghui63 panicle, score: 97.329 N N N N
vg0820097251 A -> G LOC_Os08g32460-LOC_Os08g32470 intergenic_region ; MODIFIER silent_mutation Average:84.917; most accessible tissue: Minghui63 panicle, score: 97.329 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)
vg0820097251 A G 0.01 0.0 0.0 0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0820097251 NA 2.18E-07 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
vg0820097251 NA 1.63E-09 mr1190 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
vg0820097251 NA 1.27E-07 mr1245 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
vg0820097251 NA 2.96E-08 mr1286 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
vg0820097251 NA 9.23E-08 mr1369 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
vg0820097251 NA 2.27E-08 mr1373 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
vg0820097251 NA 1.86E-06 mr1382 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
vg0820097251 NA 3.39E-06 mr1425 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
vg0820097251 NA 2.61E-08 mr1445 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
vg0820097251 NA 6.55E-10 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
vg0820097251 NA 7.70E-12 mr1522 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
vg0820097251 NA 2.09E-06 mr1574 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
vg0820097251 NA 7.87E-06 mr1633 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
vg0820097251 NA 5.03E-09 mr1652 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
vg0820097251 NA 5.67E-07 mr1665 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
vg0820097251 NA 8.92E-10 mr1730 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
vg0820097251 NA 2.41E-06 mr1830 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
vg0820097251 9.39E-06 2.51E-07 mr1224_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
vg0820097251 NA 4.68E-06 mr1404_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
vg0820097251 NA 3.28E-06 mr1620_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