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Detailed information for vg0103667899:

Variant ID: vg0103667899 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 3667899
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.01, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


CGTCTGCCGCAAAATCCATGAATTTTGGGGGTAGAAGCTCTGACGAAACGGATTTCGGTGTGTCGACGTTCTGTGATGCCTCCCATTTCTCCGCGAGACC[G/A]
TCCCCTTCCAGCATTCTGATCACCTCCGACATTCTGGGACGATGAGATGGGTAGTATTGTGTGCACAGCAAGGCCACCTGAACCATTTCCTCGAGCTCGA

Reverse complement sequence

TCGAGCTCGAGGAAATGGTTCAGGTGGCCTTGCTGTGCACACAATACTACCCATCTCATCGTCCCAGAATGTCGGAGGTGATCAGAATGCTGGAAGGGGA[C/T]
GGTCTCGCGGAGAAATGGGAGGCATCACAGAACGTCGACACACCGAAATCCGTTTCGTCAGAGCTTCTACCCCCAAAATTCATGGATTTTGCGGCAGACG

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 54.80% 44.80% 0.36% 0.11% NA
All Indica  2759 26.50% 72.90% 0.43% 0.18% NA
All Japonica  1512 96.40% 3.40% 0.26% 0.00% NA
Aus  269 93.70% 6.30% 0.00% 0.00% NA
Indica I  595 53.10% 45.40% 1.18% 0.34% NA
Indica II  465 5.60% 94.40% 0.00% 0.00% NA
Indica III  913 24.00% 75.70% 0.22% 0.11% NA
Indica Intermediate  786 21.80% 77.60% 0.38% 0.25% NA
Temperate Japonica  767 95.00% 4.80% 0.13% 0.00% NA
Tropical Japonica  504 97.60% 2.00% 0.40% 0.00% NA
Japonica Intermediate  241 97.90% 1.70% 0.41% 0.00% NA
VI/Aromatic  96 95.80% 3.10% 1.04% 0.00% NA
Intermediate  90 61.10% 38.90% 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
vg0103667899 G -> A LOC_Os01g07630.1 synonymous_variant ; p.Asp580Asp; LOW synonymous_codon Average:62.684; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N
vg0103667899 G -> DEL LOC_Os01g07630.1 N frameshift_variant Average:62.684; most accessible tissue: Zhenshan97 panicle, score: 86.432 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)
vg0103667899 G A -0.01 -0.02 -0.02 -0.03 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0103667899 NA 4.12E-07 mr1527 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
vg0103667899 NA 3.90E-07 mr1302_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
vg0103667899 NA 2.77E-06 mr1389_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
vg0103667899 NA 7.55E-08 mr1659_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
vg0103667899 NA 8.03E-07 mr1824_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