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Detailed information for vg0825984301:

Variant ID: vg0825984301 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25984301
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


GTTAACATGTTGGCAATAATCTTGCAAGCGACCGATATCTATATGTAAAGTTTTTAACTCTCAATCCGTTTTTTAATCTCTTCAATAATTAACGGGAAGT[C/T]
CTGCCTAAGATGAAAGTAGCCATTGGTGACGGCCACCTTCTTGAAGTTGCTCTCCGCCATCAAGAAGTTGAGGCACTTGCTCTTTAGCTCCGGGCAATGG

Reverse complement sequence

CCATTGCCCGGAGCTAAAGAGCAAGTGCCTCAACTTCTTGATGGCGGAGAGCAACTTCAAGAAGGTGGCCGTCACCAATGGCTACTTTCATCTTAGGCAG[G/A]
ACTTCCCGTTAATTATTGAAGAGATTAAAAAACGGATTGAGAGTTAAAAACTTTACATATAGATATCGGTCGCTTGCAAGATTATTGCCAACATGTTAAC

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 58.10% 41.60% 0.17% 0.15% NA
All Indica  2759 95.60% 4.00% 0.18% 0.22% NA
All Japonica  1512 2.20% 97.80% 0.07% 0.00% NA
Aus  269 13.40% 86.20% 0.37% 0.00% NA
Indica I  595 98.20% 1.30% 0.17% 0.34% NA
Indica II  465 96.30% 3.40% 0.22% 0.00% NA
Indica III  913 95.20% 4.60% 0.00% 0.22% NA
Indica Intermediate  786 93.80% 5.60% 0.38% 0.25% NA
Temperate Japonica  767 2.30% 97.50% 0.13% 0.00% NA
Tropical Japonica  504 1.40% 98.60% 0.00% 0.00% NA
Japonica Intermediate  241 3.30% 96.70% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 43.30% 54.40% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0825984301 C -> T LOC_Os08g41120.1 missense_variant ; p.Asp327Asn; MODERATE nonsynonymous_codon ; D327N Average:87.554; most accessible tissue: Zhenshan97 young leaf, score: 92.818 unknown unknown TOLERATED 0.17
vg0825984301 C -> DEL LOC_Os08g41120.1 N frameshift_variant Average:87.554; most accessible tissue: Zhenshan97 young leaf, score: 92.818 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)
vg0825984301 C T -0.01 0.0 0.01 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0825984301 NA 1.61E-26 mr1037 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
vg0825984301 NA 7.26E-47 mr1109 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
vg0825984301 NA 1.40E-39 mr1139 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
vg0825984301 NA 2.32E-61 mr1246 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
vg0825984301 NA 1.33E-17 mr1255 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
vg0825984301 NA 2.09E-09 mr1299 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
vg0825984301 NA 1.68E-43 mr1591 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
vg0825984301 NA 2.45E-13 mr1655 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
vg0825984301 NA 2.85E-11 mr1657 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
vg0825984301 NA 1.94E-09 mr1663 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
vg0825984301 NA 3.20E-43 mr1721 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
vg0825984301 NA 1.07E-06 mr1756 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
vg0825984301 NA 5.84E-50 mr1798 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
vg0825984301 NA 2.24E-35 mr1828 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
vg0825984301 NA 1.63E-23 mr1862 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
vg0825984301 NA 4.14E-17 mr1913 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
vg0825984301 NA 3.72E-32 mr1037_2 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
vg0825984301 NA 5.91E-21 mr1164_2 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
vg0825984301 NA 3.76E-25 mr1943_2 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