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Detailed information for vg0617915677:

Variant ID: vg0617915677 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 17915677
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGATAAAACATGAATAGTACTTTATGTGTGATTAAATATTTTCAAATTTTTCACAAATTTTTCAAATAAGACGGACGGTCAAACGTTGGGTACGGATAT[T/C]
CACGACTGCACTTATTTTGGAACGGAGGTAGTTCTGTAAATAGACGCTACTAGGTGCTTGTAGTAATTAATTAAGTAATTAAACACTAGTGCTACTGGGT

Reverse complement sequence

ACCCAGTAGCACTAGTGTTTAATTACTTAATTAATTACTACAAGCACCTAGTAGCGTCTATTTACAGAACTACCTCCGTTCCAAAATAAGTGCAGTCGTG[A/G]
ATATCCGTACCCAACGTTTGACCGTCCGTCTTATTTGAAAAATTTGTGAAAAATTTGAAAATATTTAATCACACATAAAGTACTATTCATGTTTTATCAT

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 76.30% 23.70% 0.00% 0.00% NA
All Indica  2759 98.40% 1.60% 0.00% 0.00% NA
All Japonica  1512 30.40% 69.60% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 97.30% 2.70% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 97.10% 2.90% 0.00% 0.00% NA
Temperate Japonica  767 5.20% 94.80% 0.00% 0.00% NA
Tropical Japonica  504 72.00% 28.00% 0.00% 0.00% NA
Japonica Intermediate  241 23.70% 76.30% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 75.60% 24.40% 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
vg0617915677 T -> C LOC_Os06g30860.1 downstream_gene_variant ; 246.0bp to feature; MODIFIER silent_mutation Average:68.624; most accessible tissue: Zhenshan97 flower, score: 90.548 N N N N
vg0617915677 T -> C LOC_Os06g30850-LOC_Os06g30860 intergenic_region ; MODIFIER silent_mutation Average:68.624; most accessible tissue: Zhenshan97 flower, score: 90.548 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)
vg0617915677 T C 0.01 -0.04 -0.06 -0.02 -0.03 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0617915677 NA 3.67E-07 mr1229 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
vg0617915677 NA 9.81E-07 mr1518 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
vg0617915677 NA 1.65E-08 mr1723 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
vg0617915677 NA 9.69E-07 mr1993 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
vg0617915677 NA 7.88E-06 mr1206_2 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
vg0617915677 4.74E-06 NA mr1410_2 Ind_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
vg0617915677 NA 2.13E-06 mr1723_2 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
vg0617915677 NA 7.92E-14 mr1769_2 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