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Detailed information for vg0419828219:

Variant ID: vg0419828219 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 19828219
Reference Allele: GAlternative Allele: A,T
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.81, G: 0.18, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


TCTGGTTGGACTCCCTCGATTATATGTCCAATCTGATTCCTATCACTCGATCGCAATACTGAATATATTGACTGCTTTAACTATGAAAACTGGTAGTACT[G/A,T]
CCTCCATCTCTAAATATTTGACGCCGTTGACTTTTCAAATATGTTTAACCGTTTGTCTTATTAAAAAAATTAAGTAATTATTAATTTCTTTTCTATCATT

Reverse complement sequence

AATGATAGAAAAGAAATTAATAATTACTTAATTTTTTTAATAAGACAAACGGTTAAACATATTTGAAAAGTCAACGGCGTCAAATATTTAGAGATGGAGG[C/T,A]
AGTACTACCAGTTTTCATAGTTAAAGCAGTCAATATATTCAGTATTGCGATCGAGTGATAGGAATCAGATTGGACATATAATCGAGGGAGTCCAACCAGA

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 48.00% 35.70% 0.34% 15.93% T: 0.02%
All Indica  2759 66.00% 6.50% 0.51% 27.00% T: 0.04%
All Japonica  1512 7.90% 91.90% 0.00% 0.20% NA
Aus  269 97.40% 2.60% 0.00% 0.00% NA
Indica I  595 89.10% 4.50% 0.00% 6.39% NA
Indica II  465 58.30% 11.20% 0.86% 29.68% NA
Indica III  913 58.50% 3.40% 0.33% 37.79% NA
Indica Intermediate  786 61.70% 8.80% 0.89% 28.50% T: 0.13%
Temperate Japonica  767 14.90% 85.10% 0.00% 0.00% NA
Tropical Japonica  504 0.40% 99.00% 0.00% 0.60% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 38.50% 59.40% 1.04% 1.04% NA
Intermediate  90 32.20% 62.20% 1.11% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0419828219 G -> DEL N N silent_mutation Average:59.242; most accessible tissue: Callus, score: 96.24 N N N N
vg0419828219 G -> A LOC_Os04g32840.1 upstream_gene_variant ; 317.0bp to feature; MODIFIER silent_mutation Average:59.242; most accessible tissue: Callus, score: 96.24 N N N N
vg0419828219 G -> A LOC_Os04g32840-LOC_Os04g32850 intergenic_region ; MODIFIER silent_mutation Average:59.242; most accessible tissue: Callus, score: 96.24 N N N N
vg0419828219 G -> T LOC_Os04g32840.1 upstream_gene_variant ; 317.0bp to feature; MODIFIER silent_mutation Average:59.242; most accessible tissue: Callus, score: 96.24 N N N N
vg0419828219 G -> T LOC_Os04g32840-LOC_Os04g32850 intergenic_region ; MODIFIER silent_mutation Average:59.242; most accessible tissue: Callus, score: 96.24 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)
vg0419828219 G A 0.0 0.05 0.05 0.04 0.03 0.03
vg0419828219 G T -0.04 -0.02 -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
vg0419828219 NA 1.95E-26 mr1130 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
vg0419828219 4.59E-06 1.63E-06 mr1371_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
vg0419828219 NA 8.29E-06 mr1371_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
vg0419828219 NA 3.27E-30 mr1631_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
vg0419828219 NA 3.26E-08 mr1645_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
vg0419828219 NA 8.47E-06 mr1655_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
vg0419828219 NA 1.19E-19 mr1657_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
vg0419828219 NA 4.67E-20 mr1712_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
vg0419828219 NA 4.73E-06 mr1712_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
vg0419828219 NA 4.33E-13 mr1717_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
vg0419828219 NA 5.36E-10 mr1756_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
vg0419828219 NA 1.41E-20 mr1900_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
vg0419828219 NA 1.56E-10 mr1946_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
vg0419828219 NA 2.29E-06 mr1946_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
vg0419828219 NA 1.56E-10 mr1948_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
vg0419828219 NA 2.29E-06 mr1948_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
vg0419828219 7.68E-06 3.27E-06 mr1977_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