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Detailed information for vg0225179124:

Variant ID: vg0225179124 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25179124
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


CTGGGAGAGACACGTTGGTCGGGAATTCACCAGAGAACTCATTGTCGCTAAGATCAAGACGTTGTAGCCTCTGGAGCTGGACCAGGGTTGCCGGGACGGC[C/A]
CCATGGAGGTTGTTGCTGGACAGGTTGAGCCACTGGAGCTGGTCCAGCTGCCCGAGCGAGACTGCCAGCTCGCCCCTTAGCTTCATGCCTTGGAGGTCCA

Reverse complement sequence

TGGACCTCCAAGGCATGAAGCTAAGGGGCGAGCTGGCAGTCTCGCTCGGGCAGCTGGACCAGCTCCAGTGGCTCAACCTGTCCAGCAACAACCTCCATGG[G/T]
GCCGTCCCGGCAACCCTGGTCCAGCTCCAGAGGCTACAACGTCTTGATCTTAGCGACAATGAGTTCTCTGGTGAATTCCCGACCAACGTGTCTCTCCCAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.20% 24.20% 0.51% 0.00% NA
All Indica  2759 84.30% 15.00% 0.62% 0.00% NA
All Japonica  1512 54.20% 45.40% 0.46% 0.00% NA
Aus  269 97.40% 2.60% 0.00% 0.00% NA
Indica I  595 79.50% 19.70% 0.84% 0.00% NA
Indica II  465 74.40% 25.60% 0.00% 0.00% NA
Indica III  913 96.40% 3.60% 0.00% 0.00% NA
Indica Intermediate  786 79.90% 18.60% 1.53% 0.00% NA
Temperate Japonica  767 30.10% 69.40% 0.52% 0.00% NA
Tropical Japonica  504 92.50% 7.10% 0.40% 0.00% NA
Japonica Intermediate  241 50.60% 49.00% 0.41% 0.00% NA
VI/Aromatic  96 80.20% 19.80% 0.00% 0.00% NA
Intermediate  90 78.90% 21.10% 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
vg0225179124 C -> A LOC_Os02g41890.1 synonymous_variant ; p.Gly123Gly; LOW synonymous_codon Average:87.135; most accessible tissue: Minghui63 flower, score: 91.184 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)
vg0225179124 C A -0.06 -0.07 -0.07 -0.09 -0.08 -0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225179124 NA 1.17E-06 mr1252 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
vg0225179124 NA 3.24E-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
vg0225179124 NA 1.27E-06 mr1229_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
vg0225179124 NA 3.03E-06 mr1233_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
vg0225179124 NA 3.36E-06 mr1359_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
vg0225179124 NA 3.33E-06 mr1389_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
vg0225179124 NA 1.00E-06 mr1441_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
vg0225179124 NA 2.26E-07 mr1482_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
vg0225179124 NA 1.79E-06 mr1555_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
vg0225179124 NA 1.08E-06 mr1671_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
vg0225179124 2.81E-07 3.58E-08 mr1957_2 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