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Detailed information for vg0219342827:

Variant ID: vg0219342827 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 19342827
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.74, A: 0.26, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


ACACCTCCGACCGCCGCTTCTCCATGCGGATGGGGACCAGCTACTTCGGGCTCTACATCGAGCCGCCCGCGTCGTCGTCCGGCGGCGGCGGCGTCGCGGC[A/G]
GCGATGTACTGGAAGCACACGGCGCTGCAGGCCAAGGCCGCGATCGTGGACGGCGGCGGCCCGACGTACGCGCGCGTGGAGCCCGACGGCTACCTCGCCA

Reverse complement sequence

TGGCGAGGTAGCCGTCGGGCTCCACGCGCGCGTACGTCGGGCCGCCGCCGTCCACGATCGCGGCCTTGGCCTGCAGCGCCGTGTGCTTCCAGTACATCGC[T/C]
GCCGCGACGCCGCCGCCGCCGGACGACGACGCGGGCGGCTCGATGTAGAGCCCGAAGTAGCTGGTCCCCATCCGCATGGAGAAGCGGCGGTCGGAGGTGT

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 51.90% 47.50% 0.53% 0.00% NA
All Indica  2759 77.80% 21.70% 0.54% 0.00% NA
All Japonica  1512 14.80% 84.80% 0.40% 0.00% NA
Aus  269 6.30% 93.70% 0.00% 0.00% NA
Indica I  595 57.10% 42.40% 0.50% 0.00% NA
Indica II  465 79.40% 20.00% 0.65% 0.00% NA
Indica III  913 93.90% 5.90% 0.22% 0.00% NA
Indica Intermediate  786 73.80% 25.30% 0.89% 0.00% NA
Temperate Japonica  767 5.30% 94.10% 0.52% 0.00% NA
Tropical Japonica  504 25.60% 74.00% 0.40% 0.00% NA
Japonica Intermediate  241 22.40% 77.60% 0.00% 0.00% NA
VI/Aromatic  96 32.30% 67.70% 0.00% 0.00% NA
Intermediate  90 41.10% 54.40% 4.44% 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
vg0219342827 A -> G LOC_Os02g32620.1 synonymous_variant ; p.Ala220Ala; LOW synonymous_codon Average:90.789; most accessible tissue: Zhenshan97 young leaf, score: 96.13 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)
vg0219342827 A G -0.01 0.0 0.0 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0219342827 NA 4.65E-06 mr1213 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
vg0219342827 NA 6.12E-06 mr1224 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
vg0219342827 NA 8.85E-08 mr1610 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
vg0219342827 NA 1.42E-15 mr1180_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
vg0219342827 NA 1.08E-06 mr1180_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
vg0219342827 NA 8.14E-06 mr1543_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
vg0219342827 NA 1.81E-08 mr1627_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
vg0219342827 NA 3.31E-09 mr1851_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
vg0219342827 NA 1.39E-07 mr1885_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