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Detailed information for vg0807842592:

Variant ID: vg0807842592 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 7842592
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, T: 0.11, others allele: 0.00, population size: 177. )

Flanking Sequence (100 bp) in Reference Genome:


GTCTTCTGTGATTTCGAAAACCATTTTGATGTAGTGTTTTTGTTTTTCTCCTTTTCTTGTCCCATTTCTGGTTCAGTCAGATCTCAGCCGCTTTGAAGCA[G/T]
ATGGCTCGTCGTTCTACCCGTCAGACCCTTGCTCCCAATCGCTTTGGTGTTGAAGAAGAGCTAGTTCAGTCAGAAATTCCCGATCAACCAGTTAACCAGA

Reverse complement sequence

TCTGGTTAACTGGTTGATCGGGAATTTCTGACTGAACTAGCTCTTCTTCAACACCAAAGCGATTGGGAGCAAGGGTCTGACGGGTAGAACGACGAGCCAT[C/A]
TGCTTCAAAGCGGCTGAGATCTGACTGAACCAGAAATGGGACAAGAAAAGGAGAAAAACAAAAACACTACATCAAAATGGTTTTCGAAATCACAGAAGAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 36.40% 27.10% 7.15% 29.37% NA
All Indica  2759 21.60% 44.30% 7.36% 26.82% NA
All Japonica  1512 68.80% 0.70% 5.36% 25.07% NA
Aus  269 14.50% 9.70% 11.90% 63.94% NA
Indica I  595 13.90% 14.50% 8.91% 62.69% NA
Indica II  465 8.60% 78.70% 6.24% 6.45% NA
Indica III  913 34.50% 39.30% 9.75% 16.43% NA
Indica Intermediate  786 20.00% 52.20% 4.07% 23.79% NA
Temperate Japonica  767 57.20% 0.90% 4.82% 37.03% NA
Tropical Japonica  504 82.50% 0.60% 1.79% 15.08% NA
Japonica Intermediate  241 77.20% 0.40% 14.52% 7.88% NA
VI/Aromatic  96 10.40% 3.10% 12.50% 73.96% NA
Intermediate  90 38.90% 21.10% 11.11% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0807842592 G -> T LOC_Os08g13190.1 missense_variant ; p.Gln96His; MODERATE nonsynonymous_codon ; Q96H Average:44.777; most accessible tissue: Minghui63 flag leaf, score: 85.67 unknown unknown DELETERIOUS 0.00
vg0807842592 G -> DEL LOC_Os08g13190.1 N frameshift_variant Average:44.777; most accessible tissue: Minghui63 flag leaf, score: 85.67 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)
vg0807842592 G T 0.0 0.0 0.0 0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0807842592 NA 8.24E-06 mr1030 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
vg0807842592 4.39E-06 NA mr1183 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
vg0807842592 7.72E-06 NA mr1183 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
vg0807842592 7.34E-07 NA mr1503 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
vg0807842592 1.50E-06 NA mr1503 Ind_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
vg0807842592 NA 1.15E-06 mr1024_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
vg0807842592 NA 7.03E-06 mr1232_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