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Detailed information for vg1107765430:

Variant ID: vg1107765430 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 7765430
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, G: 0.08, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


CTTGTGATGTTATGCCAAAAATCGTGCGTCCAAATATTCAGTTTGTTAATCAAACTATCATGGTGAGACGGAACAAAAGAATATGTACATTTACTACTAC[A/G]
CACATCGTTTTCCCGTGCGGTTAATTTGGATTTTCACGTACGGAGCTTCGGCCCGTCTGGAGCAATTCATCTGCGAAAATCACCATTTTTGCGTGCGGTG

Reverse complement sequence

CACCGCACGCAAAAATGGTGATTTTCGCAGATGAATTGCTCCAGACGGGCCGAAGCTCCGTACGTGAAAATCCAAATTAACCGCACGGGAAAACGATGTG[T/C]
GTAGTAGTAAATGTACATATTCTTTTGTTCCGTCTCACCATGATAGTTTGATTAACAAACTGAATATTTGGACGCACGATTTTTGGCATAACATCACAAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.00% 43.50% 0.80% 1.63% NA
All Indica  2759 86.30% 9.90% 1.34% 2.50% NA
All Japonica  1512 8.40% 91.40% 0.00% 0.20% NA
Aus  269 2.60% 97.00% 0.00% 0.37% NA
Indica I  595 86.60% 12.30% 1.01% 0.17% NA
Indica II  465 94.60% 4.30% 0.43% 0.65% NA
Indica III  913 84.90% 7.90% 1.53% 5.70% NA
Indica Intermediate  786 82.70% 13.70% 1.91% 1.65% NA
Temperate Japonica  767 3.80% 96.10% 0.00% 0.13% NA
Tropical Japonica  504 11.70% 88.10% 0.00% 0.20% NA
Japonica Intermediate  241 16.20% 83.40% 0.00% 0.41% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 41.10% 53.30% 1.11% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1107765430 A -> DEL N N silent_mutation Average:56.97; most accessible tissue: Minghui63 panicle, score: 80.641 N N N N
vg1107765430 A -> G LOC_Os11g13990.1 upstream_gene_variant ; 3033.0bp to feature; MODIFIER silent_mutation Average:56.97; most accessible tissue: Minghui63 panicle, score: 80.641 N N N N
vg1107765430 A -> G LOC_Os11g13990-LOC_Os11g14000 intergenic_region ; MODIFIER silent_mutation Average:56.97; most accessible tissue: Minghui63 panicle, score: 80.641 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)
vg1107765430 A G 0.0 -0.01 -0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1107765430 NA 7.33E-13 mr1183 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
vg1107765430 NA 1.15E-33 mr1224 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
vg1107765430 NA 3.24E-07 mr1224 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
vg1107765430 NA 2.96E-32 mr1225 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
vg1107765430 NA 1.31E-12 mr1503 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
vg1107765430 NA 1.63E-12 mr1914 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
vg1107765430 NA 3.74E-10 mr1047_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
vg1107765430 NA 2.35E-50 mr1063_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
vg1107765430 NA 4.47E-17 mr1180_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
vg1107765430 NA 1.48E-06 mr1180_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
vg1107765430 NA 3.37E-22 mr1183_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
vg1107765430 NA 2.82E-12 mr1189_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
vg1107765430 NA 1.73E-16 mr1260_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
vg1107765430 NA 9.39E-06 mr1425_2 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
vg1107765430 NA 5.60E-11 mr1728_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
vg1107765430 NA 9.17E-11 mr1734_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
vg1107765430 NA 5.00E-07 mr1834_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