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Detailed information for vg0224592034:

Variant ID: vg0224592034 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24592034
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


AGAGCAATTTTTTTTTTTGAAACCTAAGCCAGCATTGCTGGTTTTATATTAAGAGAGGGAGAAACTGTACAGACAAGAGACAACGACCCAATTTATAAGG[G/A]
AAATCAGGCCCGAAAACCATACAGCTGCACGGTTAATTATGGGGAACCGGCTAAAACCCAACGGACAGAAGAAAGCATGGGACCTAACACACAACTAACA

Reverse complement sequence

TGTTAGTTGTGTGTTAGGTCCCATGCTTTCTTCTGTCCGTTGGGTTTTAGCCGGTTCCCCATAATTAACCGTGCAGCTGTATGGTTTTCGGGCCTGATTT[C/T]
CCTTATAAATTGGGTCGTTGTCTCTTGTCTGTACAGTTTCTCCCTCTCTTAATATAAAACCAGCAATGCTGGCTTAGGTTTCAAAAAAAAAAATTGCTCT

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 87.80% 12.10% 0.13% 0.00% NA
All Indica  2759 91.90% 8.00% 0.07% 0.00% NA
All Japonica  1512 81.00% 18.80% 0.13% 0.00% NA
Aus  269 92.90% 6.30% 0.74% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 82.40% 17.40% 0.22% 0.00% NA
Indica III  913 91.30% 8.70% 0.00% 0.00% NA
Indica Intermediate  786 92.10% 7.80% 0.13% 0.00% NA
Temperate Japonica  767 78.00% 21.80% 0.26% 0.00% NA
Tropical Japonica  504 85.50% 14.50% 0.00% 0.00% NA
Japonica Intermediate  241 81.30% 18.70% 0.00% 0.00% NA
VI/Aromatic  96 66.70% 33.30% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 0.00% 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
vg0224592034 G -> A LOC_Os02g40550.1 upstream_gene_variant ; 3141.0bp to feature; MODIFIER silent_mutation Average:74.753; most accessible tissue: Zhenshan97 panicle, score: 91.536 N N N N
vg0224592034 G -> A LOC_Os02g40540.1 downstream_gene_variant ; 302.0bp to feature; MODIFIER silent_mutation Average:74.753; most accessible tissue: Zhenshan97 panicle, score: 91.536 N N N N
vg0224592034 G -> A LOC_Os02g40530-LOC_Os02g40540 intergenic_region ; MODIFIER silent_mutation Average:74.753; most accessible tissue: Zhenshan97 panicle, score: 91.536 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)
vg0224592034 G A -0.02 -0.02 -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
vg0224592034 NA 8.82E-06 mr1224 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
vg0224592034 NA 1.48E-06 mr1225 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
vg0224592034 NA 7.08E-07 mr1227 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
vg0224592034 NA 4.44E-06 mr1254 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
vg0224592034 NA 3.82E-07 mr1382 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
vg0224592034 1.71E-06 1.72E-06 mr1429 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
vg0224592034 NA 5.82E-06 mr1445 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
vg0224592034 5.56E-07 5.59E-07 mr1452 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
vg0224592034 2.89E-06 1.58E-06 mr1513 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
vg0224592034 2.18E-06 1.16E-06 mr1590 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
vg0224592034 NA 2.48E-06 mr1964 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