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Detailed information for vg0719120986:

Variant ID: vg0719120986 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 19120986
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

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

Flanking Sequence (100 bp) in Reference Genome:


GTTTAGAAACTTTTGCATAAAATGCACCGTTTAGCAGTTTGAAAAGCGTGTGAGTGAAAAACAAGGGAGAGGGGGTAGGAAAAGGGGTGCCGAACACAGC[C/G]
TTAGGATGGCTATGCACCAGGTGATGTGATATGGCAGCTTGCGGTTTTCCCCTTTGGCATGCATGCTGCGGAGTGCTACCGTGGTGCCGCCGGGTAAAAT

Reverse complement sequence

ATTTTACCCGGCGGCACCACGGTAGCACTCCGCAGCATGCATGCCAAAGGGGAAAACCGCAAGCTGCCATATCACATCACCTGGTGCATAGCCATCCTAA[G/C]
GCTGTGTTCGGCACCCCTTTTCCTACCCCCTCTCCCTTGTTTTTCACTCACACGCTTTTCAAACTGCTAAACGGTGCATTTTATGCAAAAGTTTCTAAAC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 73.60% 21.00% 5.46% 0.00% NA
All Indica  2759 55.40% 35.50% 9.10% 0.00% NA
All Japonica  1512 99.80% 0.10% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 12.40% 63.90% 23.70% 0.00% NA
Indica II  465 73.10% 17.20% 9.68% 0.00% NA
Indica III  913 71.30% 27.20% 1.53% 0.00% NA
Indica Intermediate  786 59.00% 34.50% 6.49% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 81.10% 13.30% 5.56% 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
vg0719120986 C -> G LOC_Os07g32180.1 upstream_gene_variant ; 3471.0bp to feature; MODIFIER silent_mutation Average:61.953; most accessible tissue: Callus, score: 92.598 N N N N
vg0719120986 C -> G LOC_Os07g32180-LOC_Os07g32190 intergenic_region ; MODIFIER silent_mutation Average:61.953; most accessible tissue: Callus, score: 92.598 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)
vg0719120986 C G 0.03 -0.01 0.0 0.05 0.05 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0719120986 NA 5.29E-10 Heading_date Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0719120986 NA 3.03E-06 mr1086 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
vg0719120986 6.32E-08 NA mr1213 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
vg0719120986 5.75E-10 7.41E-10 mr1213 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
vg0719120986 NA 9.57E-06 mr1246 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
vg0719120986 7.89E-06 NA mr1404 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
vg0719120986 NA 4.88E-06 mr1404 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
vg0719120986 NA 6.35E-06 mr1233_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