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Detailed information for vg0920309265:

Variant ID: vg0920309265 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 20309265
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACAGGTGCCCTCTATAATGCCATTAGTGTGCCGTGAAACGTGCCAAATATATGTCCCCCTTTCTTTTGCTGACAACCCTTGAAACACTACCAGAAACATG[T/A]
TGGTTCCTATAACGTTTGATCTTGCTTTACATGCTTTCACGTTTACTCATATAAGTTCCAATTTTACATTGTCCAAAACAAACGGTAGGGCGCCGCGAAG

Reverse complement sequence

CTTCGCGGCGCCCTACCGTTTGTTTTGGACAATGTAAAATTGGAACTTATATGAGTAAACGTGAAAGCATGTAAAGCAAGATCAAACGTTATAGGAACCA[A/T]
CATGTTTCTGGTAGTGTTTCAAGGGTTGTCAGCAAAAGAAAGGGGGACATATATTTGGCACGTTTCACGGCACACTAATGGCATTATAGAGGGCACCTGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.20% 9.80% 2.07% 17.88% NA
All Indica  2759 56.90% 16.50% 1.74% 24.79% NA
All Japonica  1512 96.60% 0.20% 1.59% 1.65% NA
Aus  269 45.00% 0.40% 7.81% 46.84% NA
Indica I  595 90.40% 1.20% 2.02% 6.39% NA
Indica II  465 90.30% 1.70% 1.08% 6.88% NA
Indica III  913 21.40% 27.30% 1.86% 49.51% NA
Indica Intermediate  786 53.20% 24.40% 1.78% 20.61% NA
Temperate Japonica  767 97.40% 0.10% 0.26% 2.22% NA
Tropical Japonica  504 95.60% 0.00% 3.97% 0.40% NA
Japonica Intermediate  241 95.90% 0.80% 0.83% 2.49% NA
VI/Aromatic  96 95.80% 1.00% 1.04% 2.08% NA
Intermediate  90 82.20% 4.40% 4.44% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0920309265 T -> DEL N N silent_mutation Average:79.254; most accessible tissue: Zhenshan97 flower, score: 93.144 N N N N
vg0920309265 T -> A LOC_Os09g34847.1 downstream_gene_variant ; 926.0bp to feature; MODIFIER silent_mutation Average:79.254; most accessible tissue: Zhenshan97 flower, score: 93.144 N N N N
vg0920309265 T -> A LOC_Os09g34850.1 downstream_gene_variant ; 4302.0bp to feature; MODIFIER silent_mutation Average:79.254; most accessible tissue: Zhenshan97 flower, score: 93.144 N N N N
vg0920309265 T -> A LOC_Os09g34847.2 downstream_gene_variant ; 1097.0bp to feature; MODIFIER silent_mutation Average:79.254; most accessible tissue: Zhenshan97 flower, score: 93.144 N N N N
vg0920309265 T -> A LOC_Os09g34850.3 downstream_gene_variant ; 4302.0bp to feature; MODIFIER silent_mutation Average:79.254; most accessible tissue: Zhenshan97 flower, score: 93.144 N N N N
vg0920309265 T -> A LOC_Os09g34850.2 downstream_gene_variant ; 4302.0bp to feature; MODIFIER silent_mutation Average:79.254; most accessible tissue: Zhenshan97 flower, score: 93.144 N N N N
vg0920309265 T -> A LOC_Os09g34847-LOC_Os09g34850 intergenic_region ; MODIFIER silent_mutation Average:79.254; most accessible tissue: Zhenshan97 flower, score: 93.144 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)
vg0920309265 T A -0.02 0.0 0.0 -0.01 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0920309265 NA 3.68E-11 mr1065 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
vg0920309265 NA 1.29E-10 mr1068 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
vg0920309265 NA 8.13E-11 mr1078 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
vg0920309265 NA 1.21E-10 mr1091 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
vg0920309265 NA 2.47E-09 mr1094 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
vg0920309265 NA 4.66E-11 mr1096 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
vg0920309265 NA 4.70E-09 mr1111 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
vg0920309265 NA 2.08E-08 mr1112 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
vg0920309265 NA 1.63E-08 mr1121 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
vg0920309265 NA 2.78E-11 mr1144 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
vg0920309265 NA 6.51E-07 mr1200 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
vg0920309265 NA 1.12E-09 mr1244 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
vg0920309265 4.83E-09 NA mr1065_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
vg0920309265 1.24E-09 3.67E-16 mr1065_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
vg0920309265 1.44E-06 NA mr1068_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
vg0920309265 4.65E-07 2.36E-14 mr1068_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
vg0920309265 3.18E-06 NA mr1078_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
vg0920309265 2.53E-06 1.32E-12 mr1078_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
vg0920309265 NA 6.88E-07 mr1090_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
vg0920309265 1.10E-06 NA mr1091_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
vg0920309265 2.51E-06 1.04E-13 mr1091_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
vg0920309265 NA 9.32E-10 mr1094_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
vg0920309265 NA 1.52E-12 mr1096_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
vg0920309265 1.61E-06 NA mr1110_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
vg0920309265 6.71E-06 1.52E-10 mr1110_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
vg0920309265 5.63E-06 NA mr1111_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
vg0920309265 3.00E-06 4.35E-13 mr1111_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
vg0920309265 NA 8.74E-11 mr1112_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
vg0920309265 3.61E-06 2.65E-12 mr1121_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
vg0920309265 2.56E-06 NA mr1144_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
vg0920309265 9.01E-07 1.08E-13 mr1144_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
vg0920309265 NA 2.67E-09 mr1200_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
vg0920309265 NA 5.80E-08 mr1211_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
vg0920309265 2.46E-06 NA mr1234_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
vg0920309265 7.50E-06 NA mr1234_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
vg0920309265 4.50E-08 NA mr1244_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
vg0920309265 1.47E-08 1.12E-15 mr1244_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