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Detailed information for vg0910768444:

Variant ID: vg0910768444 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 10768444
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


TCCCAAAACGAACAAGCAAGAAAGAGTGAAGACCTGGTCCTGACTCTGGCTCCTGAAACGGCTCGATGGAGACCTCGTAAACTGGACCAAAATTTGATCT[A/G]
TCAATCTTGGTTCCATCCAGATTTTACCTTAATTTCCATTAGCATATTTTTCAAACTACTATATGGTGTATCTATAAATTTCTATACGGAAGTGGATTTA

Reverse complement sequence

TAAATCCACTTCCGTATAGAAATTTATAGATACACCATATAGTAGTTTGAAAAATATGCTAATGGAAATTAAGGTAAAATCTGGATGGAACCAAGATTGA[T/C]
AGATCAAATTTTGGTCCAGTTTACGAGGTCTCCATCGAGCCGTTTCAGGAGCCAGAGTCAGGACCAGGTCTTCACTCTTTCTTGCTTGTTCGTTTTGGGA

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 87.90% 12.00% 0.02% 0.00% NA
All Indica  2759 80.60% 19.40% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 89.20% 10.80% 0.00% 0.00% NA
Indica I  595 95.30% 4.70% 0.00% 0.00% NA
Indica II  465 86.70% 13.30% 0.00% 0.00% NA
Indica III  913 65.10% 34.90% 0.00% 0.00% NA
Indica Intermediate  786 83.80% 16.00% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 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
vg0910768444 A -> G LOC_Os09g17610.1 upstream_gene_variant ; 422.0bp to feature; MODIFIER silent_mutation Average:74.049; most accessible tissue: Callus, score: 89.014 N N N N
vg0910768444 A -> G LOC_Os09g17600.1 downstream_gene_variant ; 176.0bp to feature; MODIFIER silent_mutation Average:74.049; most accessible tissue: Callus, score: 89.014 N N N N
vg0910768444 A -> G LOC_Os09g17620.1 downstream_gene_variant ; 1103.0bp to feature; MODIFIER silent_mutation Average:74.049; most accessible tissue: Callus, score: 89.014 N N N N
vg0910768444 A -> G LOC_Os09g17600.3 downstream_gene_variant ; 176.0bp to feature; MODIFIER silent_mutation Average:74.049; most accessible tissue: Callus, score: 89.014 N N N N
vg0910768444 A -> G LOC_Os09g17600.2 downstream_gene_variant ; 176.0bp to feature; MODIFIER silent_mutation Average:74.049; most accessible tissue: Callus, score: 89.014 N N N N
vg0910768444 A -> G LOC_Os09g17600-LOC_Os09g17610 intergenic_region ; MODIFIER silent_mutation Average:74.049; most accessible tissue: Callus, score: 89.014 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)
vg0910768444 A G 0.04 0.06 0.05 0.03 0.05 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0910768444 1.73E-06 1.73E-06 mr1054 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
vg0910768444 NA 1.63E-06 mr1072 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
vg0910768444 NA 7.33E-06 mr1124 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
vg0910768444 NA 6.07E-06 mr1286 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
vg0910768444 4.25E-06 4.25E-06 mr1287 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
vg0910768444 NA 7.77E-06 mr1293 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
vg0910768444 7.67E-06 7.67E-06 mr1293 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
vg0910768444 4.75E-06 4.75E-06 mr1294 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
vg0910768444 3.69E-06 3.69E-06 mr1299 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
vg0910768444 1.07E-06 1.07E-06 mr1340 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
vg0910768444 1.91E-06 1.11E-06 mr1372 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
vg0910768444 9.16E-06 NA mr1427 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
vg0910768444 5.17E-07 4.21E-08 mr1427 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
vg0910768444 4.50E-06 4.50E-06 mr1429 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
vg0910768444 1.24E-06 2.37E-06 mr1432 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
vg0910768444 7.42E-06 3.66E-06 mr1433 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
vg0910768444 NA 3.26E-06 mr1509 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
vg0910768444 2.52E-06 1.83E-06 mr1640 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
vg0910768444 3.06E-06 3.06E-06 mr1640 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
vg0910768444 NA 3.45E-06 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
vg0910768444 8.81E-06 9.05E-06 mr1665 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
vg0910768444 3.35E-06 NA mr1700 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
vg0910768444 1.61E-07 1.61E-07 mr1700 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
vg0910768444 1.30E-06 1.30E-06 mr1776 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
vg0910768444 NA 6.32E-06 mr1952 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
vg0910768444 2.57E-06 2.57E-06 mr1972 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