Search for Variation information by Variation ID:

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

Detailed information for vg0602958934:

Variant ID: vg0602958934 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 2958934
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


CATTAAAAACATAAAGTAGATCCATACTACTCCAAGTAATGCTTTCTTCTTTCGCAAACTACGAACTACCATAGTATACGATGTCAAGTTTTTCGGCCGG[T/A]
ACCGATACCGGGTGTACTTAGCAAATTCCTCCTGATCTCCCAGTAATAGCACTAGTACGATGATGAGTATGACCAAAGACTGGTCAACGGGGAGCAAGCA

Reverse complement sequence

TGCTTGCTCCCCGTTGACCAGTCTTTGGTCATACTCATCATCGTACTAGTGCTATTACTGGGAGATCAGGAGGAATTTGCTAAGTACACCCGGTATCGGT[A/T]
CCGGCCGAAAAACTTGACATCGTATACTATGGTAGTTCGTAGTTTGCGAAAGAAGAAAGCATTACTTGGAGTAGTATGGATCTACTTTATGTTTTTAATG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.30% 4.10% 0.53% 0.00% NA
All Indica  2759 92.30% 7.00% 0.69% 0.00% NA
All Japonica  1512 99.50% 0.10% 0.33% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 78.00% 19.70% 2.35% 0.00% NA
Indica II  465 96.60% 3.00% 0.43% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 91.70% 7.90% 0.38% 0.00% NA
Temperate Japonica  767 99.30% 0.10% 0.52% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg0602958934 T -> A LOC_Os06g06360.1 upstream_gene_variant ; 57.0bp to feature; MODIFIER silent_mutation Average:88.249; most accessible tissue: Callus, score: 99.125 N N N N
vg0602958934 T -> A LOC_Os06g06350.1 downstream_gene_variant ; 1092.0bp to feature; MODIFIER silent_mutation Average:88.249; most accessible tissue: Callus, score: 99.125 N N N N
vg0602958934 T -> A LOC_Os06g06350.2 downstream_gene_variant ; 1092.0bp to feature; MODIFIER silent_mutation Average:88.249; most accessible tissue: Callus, score: 99.125 N N N N
vg0602958934 T -> A LOC_Os06g06350-LOC_Os06g06360 intergenic_region ; MODIFIER silent_mutation Average:88.249; most accessible tissue: Callus, score: 99.125 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)
vg0602958934 T A -0.02 -0.03 -0.02 -0.02 -0.02 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0602958934 NA 4.20E-06 mr1004 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
vg0602958934 3.59E-06 NA mr1005 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
vg0602958934 NA 3.58E-07 mr1005 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
vg0602958934 NA 8.57E-09 mr1011 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
vg0602958934 NA 5.77E-07 mr1011 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
vg0602958934 2.98E-06 2.97E-06 mr1012 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
vg0602958934 NA 9.02E-06 mr1012 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
vg0602958934 NA 8.84E-06 mr1706 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
vg0602958934 NA 2.98E-08 mr1629_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
vg0602958934 NA 2.13E-06 mr1968_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