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Detailed information for vg1004381963:

Variant ID: vg1004381963 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4381963
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.51, A: 0.49, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


GCCATGATCTTGATTTACTGGACCCAATCTTTGATGAACAGAAACTCGTATTTGTGGCGCATGTGTGTCGATTTCACAGACCTGAACAAGGCATGTCCGA[T/A]
GGACGATTTCCCCTTGCCACGGATCGACTAACTCGTGGATTCGACAGCTGGCTGAGAACTCATGAGCTTCTTAGATGCATACTCCGGCTATCACCAGATC

Reverse complement sequence

GATCTGGTGATAGCCGGAGTATGCATCTAAGAAGCTCATGAGTTCTCAGCCAGCTGTCGAATCCACGAGTTAGTCGATCCGTGGCAAGGGGAAATCGTCC[A/T]
TCGGACATGCCTTGTTCAGGTCTGTGAAATCGACACACATGCGCCACAAATACGAGTTTCTGTTCATCAAAGATTGGGTCCAGTAAATCAAGATCATGGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 29.10% 27.20% 0.25% 43.48% NA
All Indica  2759 18.60% 27.20% 0.36% 53.82% NA
All Japonica  1512 54.50% 14.20% 0.13% 31.15% NA
Aus  269 0.40% 94.10% 0.00% 5.58% NA
Indica I  595 35.10% 43.40% 0.17% 21.34% NA
Indica II  465 20.90% 25.60% 0.43% 53.12% NA
Indica III  913 2.50% 20.70% 0.22% 76.56% NA
Indica Intermediate  786 23.50% 23.40% 0.64% 52.42% NA
Temperate Japonica  767 81.90% 7.70% 0.00% 10.43% NA
Tropical Japonica  504 19.20% 15.50% 0.40% 64.88% NA
Japonica Intermediate  241 41.10% 32.40% 0.00% 26.56% NA
VI/Aromatic  96 11.50% 39.60% 0.00% 48.96% NA
Intermediate  90 25.60% 33.30% 0.00% 41.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1004381963 T -> A LOC_Os10g08090.1 upstream_gene_variant ; 359.0bp to feature; MODIFIER silent_mutation Average:55.565; most accessible tissue: Zhenshan97 flag leaf, score: 84.998 N N N N
vg1004381963 T -> A LOC_Os10g08100.1 upstream_gene_variant ; 467.0bp to feature; MODIFIER silent_mutation Average:55.565; most accessible tissue: Zhenshan97 flag leaf, score: 84.998 N N N N
vg1004381963 T -> A LOC_Os10g08080.1 downstream_gene_variant ; 4641.0bp to feature; MODIFIER silent_mutation Average:55.565; most accessible tissue: Zhenshan97 flag leaf, score: 84.998 N N N N
vg1004381963 T -> A LOC_Os10g08110.1 downstream_gene_variant ; 4156.0bp to feature; MODIFIER silent_mutation Average:55.565; most accessible tissue: Zhenshan97 flag leaf, score: 84.998 N N N N
vg1004381963 T -> A LOC_Os10g08090-LOC_Os10g08100 intergenic_region ; MODIFIER silent_mutation Average:55.565; most accessible tissue: Zhenshan97 flag leaf, score: 84.998 N N N N
vg1004381963 T -> DEL N N silent_mutation Average:55.565; most accessible tissue: Zhenshan97 flag leaf, score: 84.998 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)
vg1004381963 T A -0.02 -0.02 -0.02 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004381963 NA 4.86E-07 mr1090 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
vg1004381963 NA 3.28E-06 mr1094 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
vg1004381963 NA 1.03E-06 mr1096 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
vg1004381963 4.02E-07 4.01E-07 mr1526 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