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Detailed information for vg0624849062:

Variant ID: vg0624849062 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 24849062
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.03, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


TCTGAGAAGCAGCTGTTTGGTAGCCAGCTTCTGAGAATCTGGAAAAACTCTGAAACCCAACTTCTCCAGCTTCTGATTTCTTATTTCTTAGTTCATTTTT[C/T]
ATAATATGTAACTACAGATTCTTAGAAGCTGTAGACTGTTTAGGGCAGCTTCTAGCAGAAGCAGCTTTTAAGAAAAGCTGTAGCTGGGACAAGCTCTTCT

Reverse complement sequence

AGAAGAGCTTGTCCCAGCTACAGCTTTTCTTAAAAGCTGCTTCTGCTAGAAGCTGCCCTAAACAGTCTACAGCTTCTAAGAATCTGTAGTTACATATTAT[G/A]
AAAAATGAACTAAGAAATAAGAAATCAGAAGCTGGAGAAGTTGGGTTTCAGAGTTTTTCCAGATTCTCAGAAGCTGGCTACCAAACAGCTGCTTCTCAGA

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 69.00% 30.90% 0.17% 0.00% NA
All Indica  2759 94.80% 5.20% 0.00% 0.00% NA
All Japonica  1512 33.30% 66.20% 0.46% 0.00% NA
Aus  269 29.40% 70.30% 0.37% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 94.80% 5.20% 0.00% 0.00% NA
Indica III  913 96.30% 3.70% 0.00% 0.00% NA
Indica Intermediate  786 89.30% 10.70% 0.00% 0.00% NA
Temperate Japonica  767 46.80% 52.50% 0.65% 0.00% NA
Tropical Japonica  504 19.20% 80.80% 0.00% 0.00% NA
Japonica Intermediate  241 19.90% 79.30% 0.83% 0.00% NA
VI/Aromatic  96 8.30% 91.70% 0.00% 0.00% NA
Intermediate  90 57.80% 42.20% 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
vg0624849062 C -> T LOC_Os06g41450.1 upstream_gene_variant ; 4302.0bp to feature; MODIFIER silent_mutation Average:90.678; most accessible tissue: Minghui63 root, score: 98.844 N N N N
vg0624849062 C -> T LOC_Os06g41460.1 upstream_gene_variant ; 1380.0bp to feature; MODIFIER silent_mutation Average:90.678; most accessible tissue: Minghui63 root, score: 98.844 N N N N
vg0624849062 C -> T LOC_Os06g41450-LOC_Os06g41460 intergenic_region ; MODIFIER silent_mutation Average:90.678; most accessible tissue: Minghui63 root, score: 98.844 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)
vg0624849062 C T 0.12 0.06 0.05 0.06 0.08 0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0624849062 NA 1.66E-09 mr1151 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
vg0624849062 NA 9.95E-09 mr1249 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
vg0624849062 NA 7.42E-09 mr1548_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