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Detailed information for vg0724760962:

Variant ID: vg0724760962 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 24760962
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, T: 0.01, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


GGGAACAAAAGAAGGCAGCAGGGGAAGAGCAGTGGAGGAGCTAATGAGGGACAGAGAAGCAACAGCAAGAGGGTGAGTTGCAGGGATGACAAAGATGGCG[T/A]
TAGCGCTGTGGGAGGACAGGAGAACTGTCCTCCCTCTTGTAGGCTGTTTGGGCCTTGGAGGCTGCCTTCCCAGAATTTATTATTTCCCTTCTTTTCACCT

Reverse complement sequence

AGGTGAAAAGAAGGGAAATAATAAATTCTGGGAAGGCAGCCTCCAAGGCCCAAACAGCCTACAAGAGGGAGGACAGTTCTCCTGTCCTCCCACAGCGCTA[A/T]
CGCCATCTTTGTCATCCCTGCAACTCACCCTCTTGCTGTTGCTTCTCTGTCCCTCATTAGCTCCTCCACTGCTCTTCCCCTGCTGCCTTCTTTTGTTCCC

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 62.10% 37.50% 0.21% 0.13% NA
All Indica  2759 91.50% 8.00% 0.33% 0.22% NA
All Japonica  1512 6.80% 93.10% 0.07% 0.00% NA
Aus  269 80.30% 19.70% 0.00% 0.00% NA
Indica I  595 90.80% 8.40% 0.50% 0.34% NA
Indica II  465 88.00% 11.40% 0.22% 0.43% NA
Indica III  913 98.80% 1.10% 0.00% 0.11% NA
Indica Intermediate  786 85.60% 13.60% 0.64% 0.13% NA
Temperate Japonica  767 12.10% 87.90% 0.00% 0.00% NA
Tropical Japonica  504 0.00% 100.00% 0.00% 0.00% NA
Japonica Intermediate  241 4.10% 95.40% 0.41% 0.00% NA
VI/Aromatic  96 53.10% 46.90% 0.00% 0.00% NA
Intermediate  90 46.70% 53.30% 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
vg0724760962 T -> DEL N N silent_mutation Average:80.54; most accessible tissue: Zhenshan97 young leaf, score: 87.723 N N N N
vg0724760962 T -> A LOC_Os07g41320.1 upstream_gene_variant ; 2737.0bp to feature; MODIFIER silent_mutation Average:80.54; most accessible tissue: Zhenshan97 young leaf, score: 87.723 N N N N
vg0724760962 T -> A LOC_Os07g41340.1 upstream_gene_variant ; 4717.0bp to feature; MODIFIER silent_mutation Average:80.54; most accessible tissue: Zhenshan97 young leaf, score: 87.723 N N N N
vg0724760962 T -> A LOC_Os07g41330.1 intron_variant ; MODIFIER silent_mutation Average:80.54; most accessible tissue: Zhenshan97 young leaf, score: 87.723 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)
vg0724760962 T A 0.02 0.03 0.02 0.02 0.05 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0724760962 NA 7.14E-06 mr1103 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
vg0724760962 NA 2.55E-09 mr1354 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
vg0724760962 NA 3.74E-10 mr1354_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
vg0724760962 NA 1.08E-14 mr1454_2 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
vg0724760962 NA 4.89E-15 mr1579_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
vg0724760962 NA 2.71E-16 mr1715_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
vg0724760962 NA 8.17E-09 mr1851_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