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Detailed information for vg0825763424:

Variant ID: vg0825763424 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25763424
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, G: 0.07, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


AGCTCTACCGGAAGCTGCTGCCGGCGGTGCAGAAGACGGATACCTACGGAGGAGTGATGCTTTGGAACAGCTACTATGACTCCATCACTCACTACGGACG[G/A]
TATGTCAGTGCCTGGGCTTAATTATAAGATTCAGAGATCAACCAACGATAATCTCTCTATATATACGTGTGCCTCCATCATCAGTCCAATCCGTGCGTGC

Reverse complement sequence

GCACGCACGGATTGGACTGATGATGGAGGCACACGTATATATAGAGAGATTATCGTTGGTTGATCTCTGAATCTTATAATTAAGCCCAGGCACTGACATA[C/T]
CGTCCGTAGTGAGTGATGGAGTCATAGTAGCTGTTCCAAAGCATCACTCCTCCGTAGGTATCCGTCTTCTGCACCGCCGGCAGCAGCTTCCGGTAGAGCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.20% 21.50% 0.38% 0.00% NA
All Indica  2759 72.90% 26.50% 0.62% 0.00% NA
All Japonica  1512 98.30% 1.70% 0.00% 0.00% NA
Aus  269 21.60% 78.40% 0.00% 0.00% NA
Indica I  595 96.80% 2.20% 1.01% 0.00% NA
Indica II  465 88.40% 11.20% 0.43% 0.00% NA
Indica III  913 42.80% 56.70% 0.44% 0.00% NA
Indica Intermediate  786 80.50% 18.80% 0.64% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 98.40% 1.60% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 6.20% 0.00% 0.00% NA
VI/Aromatic  96 72.90% 27.10% 0.00% 0.00% NA
Intermediate  90 75.60% 23.30% 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
vg0825763424 G -> A LOC_Os08g40690.1 synonymous_variant ; p.Arg309Arg; LOW synonymous_codon Average:68.702; most accessible tissue: Minghui63 panicle, score: 87.238 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)
vg0825763424 G A 0.0 -0.01 -0.01 -0.05 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0825763424 NA 3.26E-16 mr1119 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
vg0825763424 NA 4.03E-06 mr1262 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
vg0825763424 NA 9.14E-09 mr1417 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
vg0825763424 NA 1.67E-08 mr1442 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
vg0825763424 NA 1.98E-06 mr1774 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
vg0825763424 NA 1.74E-20 mr1817 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