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Detailed information for vg0225196844:

Variant ID: vg0225196844 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25196844
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.87, A: 0.14, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


CGCCGCTGCACGTCGTGCGGGGGCCCGGGGAGGCGGGGCGGCACGGCGTGCTGTTCTTCAGCGTGCCCGGGAAGATCGCGTGCTACGACGCCGAGAGCCG[G/A]
GCGGTCTCGGTGGTCTGGCAGGACACGGCGACGACGTCGTCGCCGAAACACTTACTGTCTTACACGTGGTTCAACTTTTATGCCTACACTCCGAGCTTTC

Reverse complement sequence

GAAAGCTCGGAGTGTAGGCATAAAAGTTGAACCACGTGTAAGACAGTAAGTGTTTCGGCGACGACGTCGTCGCCGTGTCCTGCCAGACCACCGAGACCGC[C/T]
CGGCTCTCGGCGTCGTAGCACGCGATCTTCCCGGGCACGCTGAAGAACAGCACGCCGTGCCGCCCCGCCTCCCCGGGCCCCCGCACGACGTGCAGCGGCG

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 68.20% 30.40% 0.11% 1.23% NA
All Indica  2759 53.80% 46.00% 0.11% 0.11% NA
All Japonica  1512 97.20% 2.50% 0.13% 0.13% NA
Aus  269 59.90% 23.00% 0.00% 17.10% NA
Indica I  595 43.00% 56.60% 0.17% 0.17% NA
Indica II  465 54.20% 45.80% 0.00% 0.00% NA
Indica III  913 53.30% 46.70% 0.00% 0.00% NA
Indica Intermediate  786 62.30% 37.20% 0.25% 0.25% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 92.90% 6.70% 0.20% 0.20% NA
Japonica Intermediate  241 97.90% 1.20% 0.41% 0.41% NA
VI/Aromatic  96 52.10% 43.80% 0.00% 4.17% NA
Intermediate  90 64.40% 32.20% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0225196844 G -> A LOC_Os02g41930.1 synonymous_variant ; p.Arg362Arg; LOW synonymous_codon Average:86.587; most accessible tissue: Minghui63 panicle, score: 95.346 N N N N
vg0225196844 G -> DEL LOC_Os02g41930.1 N frameshift_variant Average:86.587; most accessible tissue: Minghui63 panicle, score: 95.346 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)
vg0225196844 G A 0.0 0.0 -0.01 0.0 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225196844 NA 5.69E-06 mr1088 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
vg0225196844 NA 6.95E-07 mr1479_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
vg0225196844 NA 4.90E-06 mr1677_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
vg0225196844 NA 3.63E-09 mr1835_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