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Detailed information for vg1004864429:

Variant ID: vg1004864429 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4864429
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

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

Flanking Sequence (100 bp) in Reference Genome:


ATCGTTAGATCTATACTACACCCGGCGGATTCAAATCCCCAAACAGGAGTAGGGTATTACCTCTCATTGAGAGGGCCTGAACCTGTCTAAATCCTTGTCT[C/T]
CGCATCCATCCACTTTTAGGTCTCGTGCGTTACCCCCTTTTATTATTGCCGAATTCATGTTTCGACACTTGGCAACAACTAACACTGTTGTTCCTTGGCA

Reverse complement sequence

TGCCAAGGAACAACAGTGTTAGTTGTTGCCAAGTGTCGAAACATGAATTCGGCAATAATAAAAGGGGGTAACGCACGAGACCTAAAAGTGGATGGATGCG[G/A]
AGACAAGGATTTAGACAGGTTCAGGCCCTCTCAATGAGAGGTAATACCCTACTCCTGTTTGGGGATTTGAATCCGCCGGGTGTAGTATAGATCTAACGAT

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 92.30% 7.50% 0.15% 0.04% NA
All Indica  2759 93.60% 6.10% 0.22% 0.07% NA
All Japonica  1512 88.60% 11.40% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 88.00% 12.00% 0.00% 0.00% NA
Indica III  913 90.50% 9.30% 0.11% 0.11% NA
Indica Intermediate  786 96.10% 3.40% 0.38% 0.13% NA
Temperate Japonica  767 94.30% 5.70% 0.00% 0.00% NA
Tropical Japonica  504 87.50% 12.30% 0.20% 0.00% NA
Japonica Intermediate  241 72.60% 27.40% 0.00% 0.00% NA
VI/Aromatic  96 87.50% 12.50% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg1004864429 C -> T LOC_Os10g08990.1 upstream_gene_variant ; 355.0bp to feature; MODIFIER silent_mutation Average:61.923; most accessible tissue: Minghui63 young leaf, score: 85.236 N N N N
vg1004864429 C -> T LOC_Os10g08980.1 downstream_gene_variant ; 4454.0bp to feature; MODIFIER silent_mutation Average:61.923; most accessible tissue: Minghui63 young leaf, score: 85.236 N N N N
vg1004864429 C -> T LOC_Os10g09000.1 downstream_gene_variant ; 3598.0bp to feature; MODIFIER silent_mutation Average:61.923; most accessible tissue: Minghui63 young leaf, score: 85.236 N N N N
vg1004864429 C -> T LOC_Os10g08990-LOC_Os10g09000 intergenic_region ; MODIFIER silent_mutation Average:61.923; most accessible tissue: Minghui63 young leaf, score: 85.236 N N N N
vg1004864429 C -> DEL N N silent_mutation Average:61.923; most accessible tissue: Minghui63 young leaf, score: 85.236 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)
vg1004864429 C T -0.02 -0.03 -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
vg1004864429 1.79E-07 1.79E-07 mr1493 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