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Detailed information for vg0105868529:

Variant ID: vg0105868529 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 5868529
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


GCCCTCCACCTCTCCCGGCCGACCGGCCTACAGCCAGAGAGAGAGAGAGGAGGAATCGAGGAAGAGAAGAGGAGGAGAGATGACTCAGCCTGACATGTGG[G/A]
GTCCACGTAGGTCCCACGCTGACTCATCCACCATGTAGGATAAAATCGGGGTCAAAACCACCAAAAGACTTATTGTGACCGGTTTTGATTAGTTCAGGGA

Reverse complement sequence

TCCCTGAACTAATCAAAACCGGTCACAATAAGTCTTTTGGTGGTTTTGACCCCGATTTTATCCTACATGGTGGATGAGTCAGCGTGGGACCTACGTGGAC[C/T]
CCACATGTCAGGCTGAGTCATCTCTCCTCCTCTTCTCTTCCTCGATTCCTCCTCTCTCTCTCTCTGGCTGTAGGCCGGTCGGCCGGGAGAGGTGGAGGGC

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 52.20% 32.40% 8.06% 7.38% NA
All Indica  2759 57.20% 20.20% 10.33% 12.32% NA
All Japonica  1512 49.20% 44.80% 5.82% 0.20% NA
Aus  269 4.80% 93.70% 1.49% 0.00% NA
Indica I  595 79.50% 13.60% 6.55% 0.34% NA
Indica II  465 57.40% 25.60% 8.82% 8.17% NA
Indica III  913 44.40% 11.60% 17.31% 26.73% NA
Indica Intermediate  786 55.10% 31.80% 5.98% 7.12% NA
Temperate Japonica  767 43.30% 47.30% 9.39% 0.00% NA
Tropical Japonica  504 66.30% 31.50% 1.79% 0.40% NA
Japonica Intermediate  241 32.40% 64.30% 2.90% 0.41% NA
VI/Aromatic  96 81.20% 18.80% 0.00% 0.00% NA
Intermediate  90 58.90% 30.00% 4.44% 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
vg0105868529 G -> A LOC_Os01g10990.1 downstream_gene_variant ; 4735.0bp to feature; MODIFIER silent_mutation Average:77.757; most accessible tissue: Zhenshan97 panicle, score: 87.451 N N N N
vg0105868529 G -> A LOC_Os01g11000.1 intron_variant ; MODIFIER silent_mutation Average:77.757; most accessible tissue: Zhenshan97 panicle, score: 87.451 N N N N
vg0105868529 G -> DEL N N silent_mutation Average:77.757; most accessible tissue: Zhenshan97 panicle, score: 87.451 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)
vg0105868529 G A 0.01 -0.05 -0.02 -0.04 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0105868529 1.13E-06 NA mr1174_2 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