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Detailed information for vg1017078947:

Variant ID: vg1017078947 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 17078947
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, A: 0.03, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


GCGACCGTGGGATCTAGCCTCCACAAGGTCGGGGGACATGGATCGATCCGACTGTTGGCCGCTGTCTCCTCTACCCTCAAGCACCAGCTGCCTCCTCGGG[T/A]
GCAGATCTAGCCTCCCCGATCATTGATGCCATTTCCTCGTCTTCTCCAGTCCAAAGCAATGGTAGCCGTCCCTATCACAAGTGCGGATCTAGGCTCTCCT

Reverse complement sequence

AGGAGAGCCTAGATCCGCACTTGTGATAGGGACGGCTACCATTGCTTTGGACTGGAGAAGACGAGGAAATGGCATCAATGATCGGGGAGGCTAGATCTGC[A/T]
CCCGAGGAGGCAGCTGGTGCTTGAGGGTAGAGGAGACAGCGGCCAACAGTCGGATCGATCCATGTCCCCCGACCTTGTGGAGGCTAGATCCCACGGTCGC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.00% 42.00% 0.00% 0.00% NA
All Indica  2759 92.20% 7.80% 0.00% 0.00% NA
All Japonica  1512 7.30% 92.70% 0.00% 0.00% NA
Aus  269 14.90% 85.10% 0.00% 0.00% NA
Indica I  595 96.80% 3.20% 0.00% 0.00% NA
Indica II  465 94.00% 6.00% 0.00% 0.00% NA
Indica III  913 89.80% 10.20% 0.00% 0.00% NA
Indica Intermediate  786 90.30% 9.70% 0.00% 0.00% NA
Temperate Japonica  767 2.10% 97.90% 0.00% 0.00% NA
Tropical Japonica  504 5.40% 94.60% 0.00% 0.00% NA
Japonica Intermediate  241 28.20% 71.80% 0.00% 0.00% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 45.60% 54.40% 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
vg1017078947 T -> A LOC_Os10g32600.1 upstream_gene_variant ; 968.0bp to feature; MODIFIER silent_mutation Average:70.33; most accessible tissue: Minghui63 young leaf, score: 86.015 N N N N
vg1017078947 T -> A LOC_Os10g32590.1 downstream_gene_variant ; 3651.0bp to feature; MODIFIER silent_mutation Average:70.33; most accessible tissue: Minghui63 young leaf, score: 86.015 N N N N
vg1017078947 T -> A LOC_Os10g32600-LOC_Os10g32620 intergenic_region ; MODIFIER silent_mutation Average:70.33; most accessible tissue: Minghui63 young leaf, score: 86.015 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)
vg1017078947 T A -0.02 -0.01 -0.02 -0.03 -0.05 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1017078947 NA 2.10E-09 mr1299 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
vg1017078947 NA 1.04E-06 mr1321 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
vg1017078947 2.45E-07 2.45E-07 mr1545 Jap_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
vg1017078947 NA 9.19E-07 mr1756 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
vg1017078947 NA 1.01E-12 mr1147_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
vg1017078947 NA 6.26E-08 mr1700_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
vg1017078947 NA 1.89E-10 mr1782_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