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Detailed information for vg0809087399:

Variant ID: vg0809087399 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 9087399
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


AGACTTTTTCTTTAAACTTCTAACTTTTTTATCATATCAAAATTTTCCTACACACGTAAACTTCTAACTTTTTCATCATATCGTTCTAATTTCAACTAAA[C/T]
TTTCAATTTTGGTGTGAACTAAACACAGCCTTAACAACTTGGACATGGAATTAGGAGGATTAATTAATTAATTTGTTTACGGCGACATCCTGTTCCATAG

Reverse complement sequence

CTATGGAACAGGATGTCGCCGTAAACAAATTAATTAATTAATCCTCCTAATTCCATGTCCAAGTTGTTAAGGCTGTGTTTAGTTCACACCAAAATTGAAA[G/A]
TTTAGTTGAAATTAGAACGATATGATGAAAAAGTTAGAAGTTTACGTGTGTAGGAAAATTTTGATATGATAAAAAAGTTAGAAGTTTAAAGAAAAAGTCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.50% 15.80% 0.32% 4.36% NA
All Indica  2759 73.80% 18.40% 0.47% 7.36% NA
All Japonica  1512 93.90% 6.00% 0.13% 0.00% NA
Aus  269 50.20% 49.80% 0.00% 0.00% NA
Indica I  595 96.00% 3.70% 0.34% 0.00% NA
Indica II  465 52.30% 33.80% 0.86% 13.12% NA
Indica III  913 69.80% 19.90% 0.55% 9.75% NA
Indica Intermediate  786 74.40% 18.60% 0.25% 6.74% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 86.70% 12.90% 0.40% 0.00% NA
Japonica Intermediate  241 92.90% 7.10% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 81.10% 15.60% 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
vg0809087399 C -> T LOC_Os08g15040.1 downstream_gene_variant ; 785.0bp to feature; MODIFIER silent_mutation Average:97.034; most accessible tissue: Zhenshan97 flag leaf, score: 98.488 N N N N
vg0809087399 C -> T LOC_Os08g15040.2 downstream_gene_variant ; 785.0bp to feature; MODIFIER silent_mutation Average:97.034; most accessible tissue: Zhenshan97 flag leaf, score: 98.488 N N N N
vg0809087399 C -> T LOC_Os08g15040-LOC_Os08g15050 intergenic_region ; MODIFIER silent_mutation Average:97.034; most accessible tissue: Zhenshan97 flag leaf, score: 98.488 N N N N
vg0809087399 C -> DEL N N silent_mutation Average:97.034; most accessible tissue: Zhenshan97 flag leaf, score: 98.488 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)
vg0809087399 C T 0.03 0.07 0.05 0.05 0.05 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0809087399 NA 8.97E-06 mr1980 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
vg0809087399 8.65E-07 1.89E-06 mr1341_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