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Detailed information for vg1002794424:

Variant ID: vg1002794424 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2794424
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTGGTTGATGTGGACTAGAGAGAAAAAAAAAAGAGAAAAATGTTTGCTACGTATAAAAGATGATTGCTCCGTATGAGTATGAGAACGATACAGAGTCGA[C/T]
TCTTAGTATTTATTAGAAATTTTTTTATTGCATTGAGTGTAATAAAGGAAAGATGACTACTAAGAAAGTATTTTGTTATATTAATGGTTAGATACCGTAT

Reverse complement sequence

ATACGGTATCTAACCATTAATATAACAAAATACTTTCTTAGTAGTCATCTTTCCTTTATTACACTCAATGCAATAAAAAAATTTCTAATAAATACTAAGA[G/A]
TCGACTCTGTATCGTTCTCATACTCATACGGAGCAATCATCTTTTATACGTAGCAAACATTTTTCTCTTTTTTTTTTCTCTCTAGTCCACATCAACCAAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.70% 7.50% 19.87% 14.01% NA
All Indica  2759 42.60% 0.20% 33.49% 23.70% NA
All Japonica  1512 77.10% 22.40% 0.33% 0.13% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 22.70% 0.00% 51.26% 26.05% NA
Indica II  465 52.70% 0.40% 26.02% 20.86% NA
Indica III  913 51.50% 0.30% 25.63% 22.56% NA
Indica Intermediate  786 41.50% 0.00% 33.59% 24.94% NA
Temperate Japonica  767 60.90% 38.50% 0.39% 0.26% NA
Tropical Japonica  504 98.20% 1.60% 0.20% 0.00% NA
Japonica Intermediate  241 84.60% 14.90% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 74.40% 7.80% 11.11% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1002794424 C -> T LOC_Os10g05600.1 downstream_gene_variant ; 75.0bp to feature; MODIFIER silent_mutation Average:79.422; most accessible tissue: Zhenshan97 panicle, score: 97.011 N N N N
vg1002794424 C -> T LOC_Os10g05590-LOC_Os10g05600 intergenic_region ; MODIFIER silent_mutation Average:79.422; most accessible tissue: Zhenshan97 panicle, score: 97.011 N N N N
vg1002794424 C -> DEL N N silent_mutation Average:79.422; most accessible tissue: Zhenshan97 panicle, score: 97.011 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)
vg1002794424 C T -0.03 0.02 0.02 0.02 0.02 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002794424 NA 2.77E-07 mr1026 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
vg1002794424 NA 1.81E-06 mr1161 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