Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0631160329:

Variant ID: vg0631160329 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 31160329
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


GATGCAAGGCACGTCGCCTAACTCGATCGCGGCACTTCCGAGCAACAATGTCAAGAAAAGGGCGGTGCGGGAGATGGGATTGGGGAAGAAAACGAGCGCG[A/T]
CGAAGAGGAAGAGGGAGGAGAAGGACCCGTAGATTCTCTCGCCACGGTGGACCTCGCCGTCTCGATCCGCCGCCACCGTGGACCTCGTTGCCCCGAGCTG

Reverse complement sequence

CAGCTCGGGGCAACGAGGTCCACGGTGGCGGCGGATCGAGACGGCGAGGTCCACCGTGGCGAGAGAATCTACGGGTCCTTCTCCTCCCTCTTCCTCTTCG[T/A]
CGCGCTCGTTTTCTTCCCCAATCCCATCTCCCGCACCGCCCTTTTCTTGACATTGTTGCTCGGAAGTGCCGCGATCGAGTTAGGCGACGTGCCTTGCATC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.00% 6.70% 0.25% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 79.00% 20.40% 0.60% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 98.40% 1.00% 0.52% 0.00% NA
Tropical Japonica  504 43.50% 56.00% 0.60% 0.00% NA
Japonica Intermediate  241 91.70% 7.50% 0.83% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 91.10% 5.60% 3.33% 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
vg0631160329 A -> T LOC_Os06g51430.1 downstream_gene_variant ; 3695.0bp to feature; MODIFIER silent_mutation Average:81.435; most accessible tissue: Minghui63 panicle, score: 91.034 N N N N
vg0631160329 A -> T LOC_Os06g51440.1 downstream_gene_variant ; 2032.0bp to feature; MODIFIER silent_mutation Average:81.435; most accessible tissue: Minghui63 panicle, score: 91.034 N N N N
vg0631160329 A -> T LOC_Os06g51450.1 downstream_gene_variant ; 1370.0bp to feature; MODIFIER silent_mutation Average:81.435; most accessible tissue: Minghui63 panicle, score: 91.034 N N N N
vg0631160329 A -> T LOC_Os06g51440-LOC_Os06g51450 intergenic_region ; MODIFIER silent_mutation Average:81.435; most accessible tissue: Minghui63 panicle, score: 91.034 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)
vg0631160329 A T 0.12 0.08 0.07 0.08 0.09 0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0631160329 NA 1.07E-06 mr1082 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
vg0631160329 NA 2.00E-07 mr1083 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
vg0631160329 8.87E-06 NA mr1103 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
vg0631160329 1.24E-08 NA mr1107 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
vg0631160329 NA 9.81E-06 mr1107 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
vg0631160329 NA 6.53E-06 mr1124 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
vg0631160329 NA 4.42E-06 mr1226 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
vg0631160329 9.81E-06 NA mr1411 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
vg0631160329 4.58E-06 NA mr1437 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
vg0631160329 NA 4.83E-08 mr1551 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
vg0631160329 2.19E-06 NA mr1233_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