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Detailed information for vg0626092324:

Variant ID: vg0626092324 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 26092324
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.66, G: 0.34, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:


GTCAACTTGATTTCCTCAATGGGCATTTTTATGTCGCATATATGCTTGCGTGCGCGCTTCATGCATGTCAATAACTTAGTATACCATACTAATCTATGTA[A/G]
TGAACCCAATCGTCTTGGAACAGCTCTCGCCATGGACGCCTTCGTGCATACAAGATAATCTTGTTTTTGTTCTTGATAATCTTGTTTTATCCAAGATTAG

Reverse complement sequence

CTAATCTTGGATAAAACAAGATTATCAAGAACAAAAACAAGATTATCTTGTATGCACGAAGGCGTCCATGGCGAGAGCTGTTCCAAGACGATTGGGTTCA[T/C]
TACATAGATTAGTATGGTATACTAAGTTATTGACATGCATGAAGCGCGCACGCAAGCATATATGCGACATAAAAATGCCCATTGAGGAAATCAAGTTGAC

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 35.20% 29.60% 0.59% 34.64% NA
All Indica  2759 2.90% 43.10% 0.94% 53.06% NA
All Japonica  1512 97.60% 1.90% 0.00% 0.53% NA
Aus  269 1.90% 52.80% 0.00% 45.35% NA
Indica I  595 0.20% 21.70% 1.68% 76.47% NA
Indica II  465 6.20% 20.00% 0.22% 73.55% NA
Indica III  913 0.50% 64.10% 1.31% 34.06% NA
Indica Intermediate  786 5.70% 48.60% 0.38% 45.29% NA
Temperate Japonica  767 99.10% 0.40% 0.00% 0.52% NA
Tropical Japonica  504 94.40% 4.80% 0.00% 0.79% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 62.50% 17.70% 0.00% 19.79% NA
Intermediate  90 46.70% 24.40% 2.22% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0626092324 A -> G LOC_Os06g43410.1 upstream_gene_variant ; 192.0bp to feature; MODIFIER silent_mutation Average:77.436; most accessible tissue: Callus, score: 98.327 N N N N
vg0626092324 A -> G LOC_Os06g43420.1 downstream_gene_variant ; 4830.0bp to feature; MODIFIER silent_mutation Average:77.436; most accessible tissue: Callus, score: 98.327 N N N N
vg0626092324 A -> G LOC_Os06g43384-LOC_Os06g43410 intergenic_region ; MODIFIER silent_mutation Average:77.436; most accessible tissue: Callus, score: 98.327 N N N N
vg0626092324 A -> DEL N N silent_mutation Average:77.436; most accessible tissue: Callus, score: 98.327 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)
vg0626092324 A G -0.09 0.0 0.02 0.01 -0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0626092324 NA 3.22E-09 mr1097 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
vg0626092324 NA 8.22E-06 mr1209 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
vg0626092324 NA 9.62E-07 mr1245 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
vg0626092324 NA 8.78E-07 mr1690 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
vg0626092324 4.89E-06 1.43E-06 mr1060_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
vg0626092324 8.75E-07 8.75E-07 mr1187_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
vg0626092324 NA 2.30E-12 mr1216_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
vg0626092324 NA 3.72E-09 mr1322_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
vg0626092324 NA 2.87E-15 mr1324_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
vg0626092324 NA 1.23E-13 mr1326_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
vg0626092324 NA 2.06E-14 mr1333_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
vg0626092324 NA 1.50E-07 mr1335_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
vg0626092324 NA 8.63E-07 mr1439_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
vg0626092324 6.56E-06 7.13E-06 mr1462_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
vg0626092324 NA 1.75E-08 mr1600_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
vg0626092324 3.11E-06 3.11E-06 mr1621_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
vg0626092324 NA 4.19E-07 mr1623_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
vg0626092324 NA 6.68E-18 mr1686_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
vg0626092324 NA 3.29E-06 mr1686_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
vg0626092324 NA 1.89E-08 mr1690_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
vg0626092324 NA 1.61E-31 mr1891_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