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Detailed information for vg0515005729:

Variant ID: vg0515005729 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 15005729
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, A: 0.01, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


AGAAGGGTTCTCTGAAAGTTAGGACTCTGAAATCTCTTCTGTTGCGTGACACCCTCACCTGCTGAAACTCTGAACATGCCAATTGCCTACCAAGTACTAC[T/C]
TGTCCCAAAATAAGTGTAGCCGTGGATATCCGTGCTTAACGTTTGACCTTCCGTCTTATTTGAAAAATTTATGAAAAATTTAAAAATATTTAGTCACGCA

Reverse complement sequence

TGCGTGACTAAATATTTTTAAATTTTTCATAAATTTTTCAAATAAGACGGAAGGTCAAACGTTAAGCACGGATATCCACGGCTACACTTATTTTGGGACA[A/G]
GTAGTACTTGGTAGGCAATTGGCATGTTCAGAGTTTCAGCAGGTGAGGGTGTCACGCAACAGAAGAGATTTCAGAGTCCTAACTTTCAGAGAACCCTTCT

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 64.40% 34.80% 0.44% 0.32% NA
All Indica  2759 86.80% 12.50% 0.40% 0.33% NA
All Japonica  1512 22.10% 77.50% 0.20% 0.20% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 93.60% 6.10% 0.00% 0.34% NA
Indica II  465 73.80% 25.80% 0.22% 0.22% NA
Indica III  913 85.10% 14.00% 0.55% 0.33% NA
Indica Intermediate  786 91.30% 7.60% 0.64% 0.38% NA
Temperate Japonica  767 5.70% 94.00% 0.13% 0.13% NA
Tropical Japonica  504 48.00% 51.40% 0.20% 0.40% NA
Japonica Intermediate  241 19.90% 79.70% 0.41% 0.00% NA
VI/Aromatic  96 3.10% 91.70% 5.21% 0.00% NA
Intermediate  90 51.10% 43.30% 2.22% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0515005729 T -> DEL N N silent_mutation Average:78.923; most accessible tissue: Zhenshan97 root, score: 97.467 N N N N
vg0515005729 T -> C LOC_Os05g25780.1 downstream_gene_variant ; 4959.0bp to feature; MODIFIER silent_mutation Average:78.923; most accessible tissue: Zhenshan97 root, score: 97.467 N N N N
vg0515005729 T -> C LOC_Os05g25784.1 downstream_gene_variant ; 281.0bp to feature; MODIFIER silent_mutation Average:78.923; most accessible tissue: Zhenshan97 root, score: 97.467 N N N N
vg0515005729 T -> C LOC_Os05g25784.2 downstream_gene_variant ; 486.0bp to feature; MODIFIER silent_mutation Average:78.923; most accessible tissue: Zhenshan97 root, score: 97.467 N N N N
vg0515005729 T -> C LOC_Os05g25780-LOC_Os05g25784 intergenic_region ; MODIFIER silent_mutation Average:78.923; most accessible tissue: Zhenshan97 root, score: 97.467 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)
vg0515005729 T C -0.06 0.0 0.01 0.07 0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0515005729 NA 1.93E-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
vg0515005729 NA 1.14E-07 mr1039 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
vg0515005729 NA 1.09E-23 mr1133 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
vg0515005729 NA 2.89E-07 mr1133 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
vg0515005729 NA 4.27E-08 mr1206 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
vg0515005729 NA 6.84E-06 mr1220 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
vg0515005729 NA 3.95E-07 mr1229 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
vg0515005729 NA 5.67E-10 mr1235 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
vg0515005729 NA 1.03E-06 mr1243 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
vg0515005729 NA 1.54E-10 mr1399 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
vg0515005729 NA 3.22E-12 mr1410 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
vg0515005729 NA 5.68E-06 mr1415 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
vg0515005729 NA 8.69E-08 mr1423 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
vg0515005729 NA 1.07E-07 mr1439 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
vg0515005729 NA 5.68E-06 mr1567 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
vg0515005729 NA 4.17E-06 mr1596 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
vg0515005729 NA 2.74E-13 mr1667 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
vg0515005729 NA 7.82E-19 mr1699 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
vg0515005729 NA 1.29E-08 mr1862 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
vg0515005729 9.33E-06 NA mr1083_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
vg0515005729 NA 1.36E-16 mr1133_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
vg0515005729 NA 6.59E-06 mr1133_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
vg0515005729 9.15E-06 NA mr1155_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
vg0515005729 3.27E-06 NA mr1226_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
vg0515005729 NA 1.13E-15 mr1301_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
vg0515005729 NA 1.72E-07 mr1399_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
vg0515005729 NA 2.15E-13 mr1410_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
vg0515005729 1.84E-06 NA mr1437_2 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
vg0515005729 1.24E-06 NA mr1437_2 Jap_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
vg0515005729 NA 2.52E-07 mr1632_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
vg0515005729 NA 1.69E-10 mr1667_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