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Detailed information for vg1018585880:

Variant ID: vg1018585880 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 18585880
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


TCCCTCCAGCCGACGACGGCTCTCCTCCTCCGTTCGCTGCCGTCCCCACAAGCGTTGGTGCCATCGTCGCGTCGTGGTGGTGGCAGTCGTTGTCGTCGTC[G/A]
TCATCGTCGCGTCGGCACCATCGGTGGGGAGGAGGGAGGAGGGAGCCGACGGCGAGGAGGGAGCCGGCAGCAGAGGCGGTGTCGCGGTCATTGTCGTCGT

Reverse complement sequence

ACGACGACAATGACCGCGACACCGCCTCTGCTGCCGGCTCCCTCCTCGCCGTCGGCTCCCTCCTCCCTCCTCCCCACCGATGGTGCCGACGCGACGATGA[C/T]
GACGACGACAACGACTGCCACCACCACGACGCGACGATGGCACCAACGCTTGTGGGGACGGCAGCGAACGGAGGAGGAGAGCCGTCGTCGGCTGGAGGGA

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 51.70% 48.10% 0.21% 0.00% NA
All Indica  2759 71.90% 27.80% 0.22% 0.00% NA
All Japonica  1512 20.80% 79.00% 0.20% 0.00% NA
Aus  269 37.20% 62.80% 0.00% 0.00% NA
Indica I  595 93.40% 6.10% 0.50% 0.00% NA
Indica II  465 37.20% 62.80% 0.00% 0.00% NA
Indica III  913 75.60% 24.30% 0.11% 0.00% NA
Indica Intermediate  786 72.00% 27.70% 0.25% 0.00% NA
Temperate Japonica  767 2.60% 97.10% 0.26% 0.00% NA
Tropical Japonica  504 53.20% 46.60% 0.20% 0.00% NA
Japonica Intermediate  241 11.20% 88.80% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 46.70% 52.20% 1.11% 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
vg1018585880 G -> A LOC_Os10g34810.1 downstream_gene_variant ; 2396.0bp to feature; MODIFIER silent_mutation Average:81.522; most accessible tissue: Minghui63 flag leaf, score: 97.221 N N N N
vg1018585880 G -> A LOC_Os10g34795-LOC_Os10g34810 intergenic_region ; MODIFIER silent_mutation Average:81.522; most accessible tissue: Minghui63 flag leaf, score: 97.221 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)
vg1018585880 G A -0.05 -0.05 -0.06 -0.04 -0.05 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1018585880 3.85E-08 NA mr1771 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
vg1018585880 NA 5.60E-07 mr1771 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
vg1018585880 1.61E-06 5.48E-21 mr1771 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
vg1018585880 5.36E-07 NA mr1784 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
vg1018585880 NA 6.39E-17 mr1784 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
vg1018585880 NA 3.36E-10 mr1800 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
vg1018585880 3.98E-09 6.98E-26 mr1862 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
vg1018585880 1.25E-06 1.25E-06 mr1862 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
vg1018585880 NA 2.90E-08 mr1862 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
vg1018585880 NA 5.19E-09 mr1050_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
vg1018585880 NA 5.95E-08 mr1399_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
vg1018585880 7.69E-07 NA mr1771_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
vg1018585880 NA 1.01E-07 mr1771_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
vg1018585880 NA 3.04E-13 mr1771_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
vg1018585880 1.18E-06 NA mr1784_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
vg1018585880 NA 1.79E-14 mr1784_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
vg1018585880 NA 4.19E-13 mr1800_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
vg1018585880 8.31E-09 NA mr1862_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
vg1018585880 5.20E-06 3.10E-09 mr1862_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
vg1018585880 NA 8.83E-13 mr1862_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