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Detailed information for vg0506497050:

Variant ID: vg0506497050 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6497050
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.08, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:


AATAGAGATAAAGACCGAGTTTAGTTCTAAACTTCGAACTTTTCCATCACATCAGAACTTTCCTACACATATAAACTTTAACTTTTTTATAATATCATTT[T/C]
AATTTTAATAAAACTTTTAATTTTAGTGTAAACTGAACACACCCAAACTGTACTAAGTAAAACGCCAAATACTAATAATTGAGCAGCTGCATGATGTAGC

Reverse complement sequence

GCTACATCATGCAGCTGCTCAATTATTAGTATTTGGCGTTTTACTTAGTACAGTTTGGGTGTGTTCAGTTTACACTAAAATTAAAAGTTTTATTAAAATT[A/G]
AAATGATATTATAAAAAAGTTAAAGTTTATATGTGTAGGAAAGTTCTGATGTGATGGAAAAGTTCGAAGTTTAGAACTAAACTCGGTCTTTATCTCTATT

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 78.80% 21.10% 0.13% 0.00% NA
All Indica  2759 83.60% 16.40% 0.04% 0.00% NA
All Japonica  1512 79.20% 20.60% 0.20% 0.00% NA
Aus  269 20.80% 79.20% 0.00% 0.00% NA
Indica I  595 77.60% 22.40% 0.00% 0.00% NA
Indica II  465 91.20% 8.80% 0.00% 0.00% NA
Indica III  913 88.70% 11.30% 0.00% 0.00% NA
Indica Intermediate  786 77.60% 22.30% 0.13% 0.00% NA
Temperate Japonica  767 98.80% 1.00% 0.13% 0.00% NA
Tropical Japonica  504 50.80% 49.00% 0.20% 0.00% NA
Japonica Intermediate  241 76.30% 23.20% 0.41% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 78.90% 18.90% 2.22% 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
vg0506497050 T -> C LOC_Os05g11470-LOC_Os05g11490 intergenic_region ; MODIFIER silent_mutation Average:93.188; most accessible tissue: Minghui63 flower, score: 95.222 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)
vg0506497050 T C -0.02 -0.02 -0.02 -0.03 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506497050 NA 8.67E-09 mr1583 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
vg0506497050 2.87E-06 2.87E-06 mr1929 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
vg0506497050 NA 2.62E-06 mr1072_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
vg0506497050 NA 1.34E-06 mr1075_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
vg0506497050 1.24E-07 5.20E-10 mr1124_2 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
vg0506497050 2.72E-06 1.32E-08 mr1850_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
vg0506497050 NA 7.94E-06 mr1865_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