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Detailed information for vg0728253524:

Variant ID: vg0728253524 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 28253524
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, G: 0.04, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


CCGGTTCTTGAGCTTGAGGCGCGCGCACAAACTGAAAAAATGCCAGCCGATCCGCCGATAAATTCCAGCTCGAAGCTAAGGCTCGATCTTTATGGCTTGC[G/T]
CACTGATCTGTGCCGCGAAAGCAGCTAAATTCAGGGAGATGTTGGGGGTGGGGGTAGGGGAAGGAAGTCAAGGCCTCGAGGGCACAAGGCTCAAGATGGC

Reverse complement sequence

GCCATCTTGAGCCTTGTGCCCTCGAGGCCTTGACTTCCTTCCCCTACCCCCACCCCCAACATCTCCCTGAATTTAGCTGCTTTCGCGGCACAGATCAGTG[C/A]
GCAAGCCATAAAGATCGAGCCTTAGCTTCGAGCTGGAATTTATCGGCGGATCGGCTGGCATTTTTTCAGTTTGTGCGCGCGCCTCAAGCTCAAGAACCGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.10% 46.40% 0.34% 0.13% NA
All Indica  2759 43.70% 55.50% 0.54% 0.18% NA
All Japonica  1512 68.10% 31.90% 0.00% 0.00% NA
Aus  269 50.60% 49.40% 0.00% 0.00% NA
Indica I  595 59.20% 40.70% 0.17% 0.00% NA
Indica II  465 24.50% 74.40% 1.08% 0.00% NA
Indica III  913 47.90% 51.60% 0.33% 0.22% NA
Indica Intermediate  786 38.70% 60.20% 0.76% 0.38% NA
Temperate Japonica  767 96.20% 3.80% 0.00% 0.00% NA
Tropical Japonica  504 22.80% 77.20% 0.00% 0.00% NA
Japonica Intermediate  241 73.40% 26.60% 0.00% 0.00% NA
VI/Aromatic  96 78.10% 20.80% 1.04% 0.00% NA
Intermediate  90 67.80% 31.10% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0728253524 G -> DEL N N silent_mutation Average:91.126; most accessible tissue: Callus, score: 97.24 N N N N
vg0728253524 G -> T LOC_Os07g47270.1 5_prime_UTR_variant ; 108.0bp to feature; MODIFIER silent_mutation Average:91.126; most accessible tissue: Callus, score: 97.24 N N N N
vg0728253524 G -> T LOC_Os07g47280.1 upstream_gene_variant ; 4877.0bp to feature; MODIFIER silent_mutation Average:91.126; most accessible tissue: Callus, score: 97.24 N N N N
vg0728253524 G -> T LOC_Os07g47260.1 downstream_gene_variant ; 3817.0bp to feature; MODIFIER silent_mutation Average:91.126; most accessible tissue: Callus, score: 97.24 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)
vg0728253524 G T -0.03 -0.06 -0.04 -0.07 -0.05 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0728253524 NA 7.43E-06 mr1075 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
vg0728253524 NA 9.77E-06 mr1077 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
vg0728253524 NA 9.70E-07 mr1124 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
vg0728253524 NA 9.27E-07 mr1277 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
vg0728253524 NA 1.15E-07 mr1551 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
vg0728253524 NA 4.10E-14 mr1879 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
vg0728253524 NA 1.22E-09 mr1304_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
vg0728253524 NA 3.43E-08 mr1308_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
vg0728253524 NA 1.33E-09 mr1361_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
vg0728253524 NA 3.82E-13 mr1368_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
vg0728253524 NA 7.80E-06 mr1449_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
vg0728253524 NA 8.04E-16 mr1540_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
vg0728253524 NA 3.07E-07 mr1551_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
vg0728253524 NA 5.03E-11 mr1584_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
vg0728253524 NA 1.55E-06 mr1730_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
vg0728253524 NA 2.83E-15 mr1732_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
vg0728253524 NA 5.63E-06 mr1853_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
vg0728253524 NA 1.09E-06 mr1866_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
vg0728253524 NA 4.33E-11 mr1879_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
vg0728253524 NA 1.62E-10 mr1942_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