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Detailed information for vg0610886119:

Variant ID: vg0610886119 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 10886119
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.02, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


TGGATTCGCGCATTGCCATCCACCTACGAAATAGCTGAGGGAGTCATTTTGAATGGTTTTAATAGTTGAGGGGTTGATATACCCGGTTTTGCGATCGAAT[T/G]
ATACAAATTAGATTTCAACCTATAATTAAGGGAGTCAAATTGGACTTTTTCCAGTCTATTTAGTGCCTGTTTGGCACGGCTCTAGCTCTAACTCCATCTC

Reverse complement sequence

GAGATGGAGTTAGAGCTAGAGCCGTGCCAAACAGGCACTAAATAGACTGGAAAAAGTCCAATTTGACTCCCTTAATTATAGGTTGAAATCTAATTTGTAT[A/C]
ATTCGATCGCAAAACCGGGTATATCAACCCCTCAACTATTAAAACCATTCAAAATGACTCCCTCAGCTATTTCGTAGGTGGATGGCAATGCGCGAATCCA

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 85.50% 13.10% 0.32% 1.02% NA
All Indica  2759 96.30% 3.00% 0.54% 0.11% NA
All Japonica  1512 65.60% 34.40% 0.00% 0.00% NA
Aus  269 84.00% 0.70% 0.00% 15.24% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 92.30% 6.20% 1.42% 0.00% NA
Indica Intermediate  786 96.90% 2.40% 0.25% 0.38% NA
Temperate Japonica  767 40.00% 60.00% 0.00% 0.00% NA
Tropical Japonica  504 97.60% 2.40% 0.00% 0.00% NA
Japonica Intermediate  241 80.10% 19.90% 0.00% 0.00% NA
VI/Aromatic  96 89.60% 7.30% 0.00% 3.12% NA
Intermediate  90 90.00% 8.90% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0610886119 T -> G LOC_Os06g19130.1 intron_variant ; MODIFIER silent_mutation Average:76.521; most accessible tissue: Zhenshan97 panicle, score: 95.493 N N N N
vg0610886119 T -> DEL N N silent_mutation Average:76.521; most accessible tissue: Zhenshan97 panicle, score: 95.493 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)
vg0610886119 T G -0.13 -0.12 -0.05 -0.09 -0.11 -0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0610886119 NA 5.12E-06 mr1087 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
vg0610886119 2.32E-06 NA mr1386_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
vg0610886119 NA 3.70E-06 mr1386_2 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
vg0610886119 3.14E-06 NA mr1585_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
vg0610886119 NA 2.58E-07 mr1980_2 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