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Detailed information for vg0421302742:

Variant ID: vg0421302742 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 21302742
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, A: 0.12, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:


AATATTTTATTTTTATTATATATATTATAATAGAAAACATAGTGAAAGATATATTTTGAAAACCATGATATTATTCAAAACGTTAACAATTATGAAAGTG[A/G]
AGAAAATAAAGGATTTACAAATATCACACGATGTACGGTTATTGGATAACTGTAATACCGTCATACCGTGAGGCAACGATAACCCTTATCAAGACGACAA

Reverse complement sequence

TTGTCGTCTTGATAAGGGTTATCGTTGCCTCACGGTATGACGGTATTACAGTTATCCAATAACCGTACATCGTGTGATATTTGTAAATCCTTTATTTTCT[T/C]
CACTTTCATAATTGTTAACGTTTTGAATAATATCATGGTTTTCAAAATATATCTTTCACTATGTTTTCTATTATAATATATATAATAAAAATAAAATATT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 68.40% 31.20% 0.40% 0.00% NA
All Indica  2759 66.00% 33.50% 0.54% 0.00% NA
All Japonica  1512 81.10% 18.80% 0.07% 0.00% NA
Aus  269 40.10% 59.90% 0.00% 0.00% NA
Indica I  595 72.90% 26.70% 0.34% 0.00% NA
Indica II  465 78.10% 21.30% 0.65% 0.00% NA
Indica III  913 53.30% 46.20% 0.44% 0.00% NA
Indica Intermediate  786 68.20% 31.00% 0.76% 0.00% NA
Temperate Japonica  767 86.60% 13.40% 0.00% 0.00% NA
Tropical Japonica  504 84.70% 15.10% 0.20% 0.00% NA
Japonica Intermediate  241 56.00% 44.00% 0.00% 0.00% NA
VI/Aromatic  96 16.70% 83.30% 0.00% 0.00% NA
Intermediate  90 71.10% 25.60% 3.33% 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
vg0421302742 A -> G LOC_Os04g35050.1 downstream_gene_variant ; 2209.0bp to feature; MODIFIER silent_mutation Average:75.14; most accessible tissue: Callus, score: 96.381 N N N N
vg0421302742 A -> G LOC_Os04g35050-LOC_Os04g35060 intergenic_region ; MODIFIER silent_mutation Average:75.14; most accessible tissue: Callus, score: 96.381 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)
vg0421302742 A G -0.02 -0.01 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0421302742 NA 1.37E-06 mr1180 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
vg0421302742 NA 3.55E-06 mr1072_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
vg0421302742 NA 3.64E-06 mr1075_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
vg0421302742 NA 2.41E-06 mr1149_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
vg0421302742 8.83E-06 8.83E-06 mr1267_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
vg0421302742 NA 1.30E-07 mr1317_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
vg0421302742 NA 7.58E-06 mr1441_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
vg0421302742 NA 2.76E-06 mr1608_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
vg0421302742 NA 8.82E-07 mr1610_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
vg0421302742 6.93E-07 2.09E-06 mr1757_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
vg0421302742 NA 2.79E-08 mr1818_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
vg0421302742 NA 9.18E-08 mr1897_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
vg0421302742 NA 5.35E-07 mr1914_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
vg0421302742 NA 3.20E-07 mr1927_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