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Detailed information for vg1203474916:

Variant ID: vg1203474916 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 3474916
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.73, A: 0.27, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


GAAATCCCCCAACTCAGTGCTCTGCCGGTCTGACCGGAGGTATGTGGCCGGTCAGACCGTGCTACTCTACAACGCCTAGTTTTCTAGCCGTTGTAGGGCT[A/G]
TCATTGGGCCCCACCGCCCTGGCCGGTCAGACCGACATGGGGTGGCCGGTCAGACCGGCCTCGGCTTGGTCAGACCACCACCAGCTCGGTCTGATCGAAT

Reverse complement sequence

ATTCGATCAGACCGAGCTGGTGGTGGTCTGACCAAGCCGAGGCCGGTCTGACCGGCCACCCCATGTCGGTCTGACCGGCCAGGGCGGTGGGGCCCAATGA[T/C]
AGCCCTACAACGGCTAGAAAACTAGGCGTTGTAGAGTAGCACGGTCTGACCGGCCACATACCTCCGGTCAGACCGGCAGAGCACTGAGTTGGGGGATTTC

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 51.60% 48.20% 0.25% 0.02% NA
All Indica  2759 80.60% 19.00% 0.36% 0.04% NA
All Japonica  1512 5.40% 94.60% 0.00% 0.00% NA
Aus  269 39.40% 60.20% 0.37% 0.00% NA
Indica I  595 82.40% 17.30% 0.34% 0.00% NA
Indica II  465 96.60% 3.20% 0.22% 0.00% NA
Indica III  913 72.50% 26.80% 0.55% 0.11% NA
Indica Intermediate  786 79.10% 20.60% 0.25% 0.00% NA
Temperate Japonica  767 1.00% 99.00% 0.00% 0.00% NA
Tropical Japonica  504 12.50% 87.50% 0.00% 0.00% NA
Japonica Intermediate  241 4.10% 95.90% 0.00% 0.00% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 24.40% 74.40% 1.11% 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
vg1203474916 A -> DEL N N silent_mutation Average:72.183; most accessible tissue: Minghui63 young leaf, score: 87.373 N N N N
vg1203474916 A -> G LOC_Os12g07080.1 downstream_gene_variant ; 2719.0bp to feature; MODIFIER silent_mutation Average:72.183; most accessible tissue: Minghui63 young leaf, score: 87.373 N N N N
vg1203474916 A -> G LOC_Os12g07100.1 downstream_gene_variant ; 4398.0bp to feature; MODIFIER silent_mutation Average:72.183; most accessible tissue: Minghui63 young leaf, score: 87.373 N N N N
vg1203474916 A -> G LOC_Os12g07080-LOC_Os12g07100 intergenic_region ; MODIFIER silent_mutation Average:72.183; most accessible tissue: Minghui63 young leaf, score: 87.373 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)
vg1203474916 A G 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1203474916 NA 2.03E-19 Yield 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
vg1203474916 NA 8.88E-07 mr1220 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
vg1203474916 NA 4.61E-08 mr1249 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
vg1203474916 NA 7.96E-10 mr1336 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
vg1203474916 NA 7.81E-06 mr1336 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
vg1203474916 NA 6.23E-12 mr1940 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
vg1203474916 NA 4.14E-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
vg1203474916 NA 4.99E-26 mr1323_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
vg1203474916 NA 6.33E-14 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
vg1203474916 NA 1.16E-15 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
vg1203474916 NA 5.77E-22 mr1336_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
vg1203474916 NA 7.82E-07 mr1336_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
vg1203474916 NA 7.24E-10 mr1338_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
vg1203474916 NA 9.57E-07 mr1346_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
vg1203474916 NA 4.92E-16 mr1454_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
vg1203474916 NA 3.07E-06 mr1559_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
vg1203474916 NA 6.79E-17 mr1579_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
vg1203474916 NA 9.72E-07 mr1579_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
vg1203474916 NA 6.45E-15 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
vg1203474916 NA 4.28E-09 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