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Detailed information for vg0507088705:

Variant ID: vg0507088705 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 7088705
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


CGGCTTTCCCGCGGGAGTCTCTCCTGAGTCTGACCAGGGTTGGACTTACCGCCGGTAACCGGTTTATCGCGGGGGTATGGTAATATAAATACTTCGGTAA[C/T]
CTTTTTAAATTCAAATAAATTTAAAAAATAATTTGAATTTTTGATAAATTTTGCACGGTTTATCACGGTTACCACGGTTACCGTGCGGTAACCGTGCTTA

Reverse complement sequence

TAAGCACGGTTACCGCACGGTAACCGTGGTAACCGTGATAAACCGTGCAAAATTTATCAAAAATTCAAATTATTTTTTAAATTTATTTGAATTTAAAAAG[G/A]
TTACCGAAGTATTTATATTACCATACCCCCGCGATAAACCGGTTACCGGCGGTAAGTCCAACCCTGGTCAGACTCAGGAGAGACTCCCGCGGGAAAGCCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.40% 33.70% 6.03% 1.82% NA
All Indica  2759 56.40% 33.20% 7.32% 3.08% NA
All Japonica  1512 61.70% 34.10% 4.10% 0.07% NA
Aus  269 80.70% 17.50% 1.86% 0.00% NA
Indica I  595 74.10% 15.00% 7.73% 3.19% NA
Indica II  465 27.50% 59.80% 8.17% 4.52% NA
Indica III  913 56.10% 33.70% 7.34% 2.85% NA
Indica Intermediate  786 60.30% 30.80% 6.49% 2.42% NA
Temperate Japonica  767 92.00% 6.40% 1.56% 0.00% NA
Tropical Japonica  504 16.70% 76.00% 7.14% 0.20% NA
Japonica Intermediate  241 59.30% 34.90% 5.81% 0.00% NA
VI/Aromatic  96 7.30% 84.40% 8.33% 0.00% NA
Intermediate  90 53.30% 37.80% 8.89% 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
vg0507088705 C -> T LOC_Os05g12330.1 upstream_gene_variant ; 184.0bp to feature; MODIFIER silent_mutation Average:88.363; most accessible tissue: Zhenshan97 panicle, score: 96.801 N N N N
vg0507088705 C -> T LOC_Os05g12340.1 upstream_gene_variant ; 1859.0bp to feature; MODIFIER silent_mutation Average:88.363; most accessible tissue: Zhenshan97 panicle, score: 96.801 N N N N
vg0507088705 C -> T LOC_Os05g12320.1 downstream_gene_variant ; 3672.0bp to feature; MODIFIER silent_mutation Average:88.363; most accessible tissue: Zhenshan97 panicle, score: 96.801 N N N N
vg0507088705 C -> T LOC_Os05g12330-LOC_Os05g12340 intergenic_region ; MODIFIER silent_mutation Average:88.363; most accessible tissue: Zhenshan97 panicle, score: 96.801 N N N N
vg0507088705 C -> DEL N N silent_mutation Average:88.363; most accessible tissue: Zhenshan97 panicle, score: 96.801 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)
vg0507088705 C T 0.05 0.04 0.04 0.06 0.05 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0507088705 NA 3.26E-16 Grain_thickness Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0507088705 NA 1.91E-12 Grain_width Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0507088705 NA 5.83E-06 mr1082 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
vg0507088705 7.01E-07 NA mr1195 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
vg0507088705 1.38E-06 2.24E-09 mr1195 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
vg0507088705 NA 2.46E-06 mr1401 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
vg0507088705 2.37E-07 NA mr1531 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
vg0507088705 7.33E-07 2.40E-10 mr1531 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
vg0507088705 NA 4.14E-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
vg0507088705 1.79E-51 2.08E-87 mr1593 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
vg0507088705 1.78E-44 3.62E-76 mr1593 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
vg0507088705 2.02E-14 2.04E-37 mr1593 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
vg0507088705 NA 2.14E-06 mr1807 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
vg0507088705 NA 9.32E-06 mr1904 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
vg0507088705 1.85E-09 NA mr1195_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
vg0507088705 5.43E-10 1.63E-20 mr1195_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
vg0507088705 NA 1.33E-06 mr1482_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
vg0507088705 2.24E-07 NA mr1531_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
vg0507088705 3.37E-08 1.87E-13 mr1531_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
vg0507088705 1.41E-54 7.27E-110 mr1593_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
vg0507088705 8.82E-43 1.77E-86 mr1593_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
vg0507088705 1.83E-21 6.58E-58 mr1593_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
vg0507088705 3.17E-07 1.37E-21 mr1807_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
vg0507088705 2.23E-06 2.33E-11 mr1807_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