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Detailed information for vg0506638245:

Variant ID: vg0506638245 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6638245
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.56, T: 0.44, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


AGTCAATTAATAGCCAATTCATACAATTGTTATCTATTGTCTGGTCCCACCTGTAATGCACACATATATCTTAGAGTCCGTGCTACAGCTGGCTACAAAT[T/C]
TGTAGCCTGCTACTCTTCTCTTTTCTCTTTTATCTCCTTAAAATATGTTTATAGCTAACTTATATAGTCTAATATTGTACCTGCTCTGATGCCGCTAGCT

Reverse complement sequence

AGCTAGCGGCATCAGAGCAGGTACAATATTAGACTATATAAGTTAGCTATAAACATATTTTAAGGAGATAAAAGAGAAAAGAGAAGAGTAGCAGGCTACA[A/G]
ATTTGTAGCCAGCTGTAGCACGGACTCTAAGATATATGTGTGCATTACAGGTGGGACCAGACAATAGATAACAATTGTATGAATTGGCTATTAATTGACT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.50% 32.40% 0.13% 0.00% NA
All Indica  2759 56.50% 43.30% 0.14% 0.00% NA
All Japonica  1512 94.60% 5.40% 0.07% 0.00% NA
Aus  269 15.60% 84.40% 0.00% 0.00% NA
Indica I  595 86.40% 13.60% 0.00% 0.00% NA
Indica II  465 55.30% 44.50% 0.22% 0.00% NA
Indica III  913 35.80% 63.90% 0.33% 0.00% NA
Indica Intermediate  786 58.70% 41.30% 0.00% 0.00% NA
Temperate Japonica  767 93.20% 6.80% 0.00% 0.00% NA
Tropical Japonica  504 96.60% 3.40% 0.00% 0.00% NA
Japonica Intermediate  241 94.60% 5.00% 0.41% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 75.60% 23.30% 1.11% 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
vg0506638245 T -> C LOC_Os05g11680-LOC_Os05g11700 intergenic_region ; MODIFIER silent_mutation Average:66.527; most accessible tissue: Zhenshan97 panicle, score: 93.351 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)
vg0506638245 T C -0.06 -0.02 -0.01 0.0 -0.07 -0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506638245 NA 4.22E-07 mr1039 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
vg0506638245 NA 1.56E-06 mr1050 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
vg0506638245 NA 5.45E-06 mr1308 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
vg0506638245 NA 7.71E-06 mr1632 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
vg0506638245 4.71E-06 4.71E-06 mr1852 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
vg0506638245 NA 1.43E-09 mr1039_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
vg0506638245 NA 2.66E-08 mr1632_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