Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0102751912:

Variant ID: vg0102751912 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 2751912
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:


CACTAAAAGACATCTTTAAATCTTAACCATTCATTCTCCCTCTTCTATTTAATACTAACCCTTCATTCATTTCTCAATCTCAATCCCACCCCACATTTCC[C/T]
ATTATCCAAACACACCCGAAATGTTTTGATCACATGGACGAAATTGGCGGGGTAGCTGGCAGTTTTAGTAGCATTAACTGCCAACTGTCCGCTGCTAATC

Reverse complement sequence

GATTAGCAGCGGACAGTTGGCAGTTAATGCTACTAAAACTGCCAGCTACCCCGCCAATTTCGTCCATGTGATCAAAACATTTCGGGTGTGTTTGGATAAT[G/A]
GGAAATGTGGGGTGGGATTGAGATTGAGAAATGAATGAAGGGTTAGTATTAAATAGAAGAGGGAGAATGAATGGTTAAGATTTAAAGATGTCTTTTAGTG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.00% 43.40% 0.57% 0.02% NA
All Indica  2759 38.50% 60.80% 0.69% 0.04% NA
All Japonica  1512 83.30% 16.50% 0.26% 0.00% NA
Aus  269 77.30% 22.70% 0.00% 0.00% NA
Indica I  595 70.90% 27.90% 1.18% 0.00% NA
Indica II  465 13.10% 86.00% 0.65% 0.22% NA
Indica III  913 34.50% 65.30% 0.22% 0.00% NA
Indica Intermediate  786 33.50% 65.60% 0.89% 0.00% NA
Temperate Japonica  767 73.50% 26.20% 0.26% 0.00% NA
Tropical Japonica  504 92.70% 7.10% 0.20% 0.00% NA
Japonica Intermediate  241 94.60% 5.00% 0.41% 0.00% NA
VI/Aromatic  96 75.00% 25.00% 0.00% 0.00% NA
Intermediate  90 50.00% 45.60% 4.44% 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
vg0102751912 C -> T LOC_Os01g05760.1 upstream_gene_variant ; 306.0bp to feature; MODIFIER silent_mutation Average:54.251; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N
vg0102751912 C -> T LOC_Os01g05770.1 upstream_gene_variant ; 1878.0bp to feature; MODIFIER silent_mutation Average:54.251; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N
vg0102751912 C -> T LOC_Os01g05744.1 downstream_gene_variant ; 4473.0bp to feature; MODIFIER silent_mutation Average:54.251; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N
vg0102751912 C -> T LOC_Os01g05744-LOC_Os01g05760 intergenic_region ; MODIFIER silent_mutation Average:54.251; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N
vg0102751912 C -> DEL N N silent_mutation Average:54.251; most accessible tissue: Minghui63 panicle, score: 74.563 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)
vg0102751912 C T 0.01 -0.02 -0.01 -0.03 -0.03 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0102751912 NA 3.70E-06 mr1026 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
vg0102751912 NA 2.60E-09 mr1174 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
vg0102751912 NA 3.94E-07 mr1503 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
vg0102751912 NA 2.59E-06 mr1826 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
vg0102751912 NA 5.49E-06 mr1036_2 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
vg0102751912 NA 5.47E-07 mr1169_2 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
vg0102751912 NA 3.95E-11 mr1174_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
vg0102751912 NA 4.54E-09 mr1174_2 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
vg0102751912 NA 1.86E-08 mr1347_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
vg0102751912 NA 5.23E-08 mr1347_2 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