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Detailed information for vg0222743406:

Variant ID: vg0222743406 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22743406
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, T: 0.01, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


GTACGGCAGTGCCACTACCTCCGCATCAAAATGAGTATAGCTATGGGCACCCGTGTACAACGTGATTGTCCGTCTTATCTACAAAATTTATAAAAAAATT[A/T]
AAAATAATTAGTTATATAGTACTGCTAATGTTTTATCATCTAACAATAATAAAAATATTATTCACAGAAAATTTTTAAATGAGATAAACGGTTAAATGTT

Reverse complement sequence

AACATTTAACCGTTTATCTCATTTAAAAATTTTCTGTGAATAATATTTTTATTATTGTTAGATGATAAAACATTAGCAGTACTATATAACTAATTATTTT[T/A]
AATTTTTTTATAAATTTTGTAGATAAGACGGACAATCACGTTGTACACGGGTGCCCATAGCTATACTCATTTTGATGCGGAGGTAGTGGCACTGCCGTAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.40% 4.30% 6.50% 2.81% NA
All Indica  2759 78.10% 7.20% 10.29% 4.39% NA
All Japonica  1512 99.70% 0.10% 0.07% 0.07% NA
Aus  269 90.00% 0.40% 6.32% 3.35% NA
Indica I  595 70.10% 0.00% 26.05% 3.87% NA
Indica II  465 63.40% 23.20% 8.17% 5.16% NA
Indica III  913 89.20% 4.10% 1.64% 5.15% NA
Indica Intermediate  786 80.20% 6.70% 9.67% 3.44% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 95.80% 0.00% 2.08% 2.08% NA
Intermediate  90 94.40% 2.20% 3.33% 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
vg0222743406 A -> T LOC_Os02g37680.1 upstream_gene_variant ; 4752.0bp to feature; MODIFIER silent_mutation Average:98.564; most accessible tissue: Zhenshan97 panicle, score: 99.545 N N N N
vg0222743406 A -> T LOC_Os02g37690.1 upstream_gene_variant ; 45.0bp to feature; MODIFIER silent_mutation Average:98.564; most accessible tissue: Zhenshan97 panicle, score: 99.545 N N N N
vg0222743406 A -> T LOC_Os02g37694.1 upstream_gene_variant ; 344.0bp to feature; MODIFIER silent_mutation Average:98.564; most accessible tissue: Zhenshan97 panicle, score: 99.545 N N N N
vg0222743406 A -> T LOC_Os02g37690-LOC_Os02g37694 intergenic_region ; MODIFIER silent_mutation Average:98.564; most accessible tissue: Zhenshan97 panicle, score: 99.545 N N N N
vg0222743406 A -> DEL N N silent_mutation Average:98.564; most accessible tissue: Zhenshan97 panicle, score: 99.545 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)
vg0222743406 A T 0.0 0.0 -0.01 0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222743406 NA 2.42E-06 mr1069 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
vg0222743406 NA 2.96E-06 mr1072 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
vg0222743406 NA 1.22E-06 mr1075 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
vg0222743406 NA 3.16E-09 mr1077 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
vg0222743406 NA 6.53E-06 mr1101 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
vg0222743406 NA 8.47E-06 mr1150 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
vg0222743406 NA 1.87E-06 mr1441 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
vg0222743406 NA 1.12E-06 mr1592 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
vg0222743406 NA 7.82E-07 mr1911 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
vg0222743406 NA 5.67E-08 mr1918 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
vg0222743406 NA 2.89E-07 mr1929 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
vg0222743406 NA 3.21E-07 mr1962 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
vg0222743406 3.57E-06 1.53E-06 mr1074_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
vg0222743406 1.88E-06 2.58E-07 mr1095_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
vg0222743406 NA 5.08E-08 mr1098_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
vg0222743406 9.20E-07 2.30E-08 mr1099_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
vg0222743406 NA 7.34E-06 mr1146_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
vg0222743406 NA 5.37E-06 mr1148_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
vg0222743406 NA 3.01E-09 mr1150_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
vg0222743406 3.65E-08 2.80E-08 mr1222_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
vg0222743406 NA 2.18E-06 mr1871_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
vg0222743406 1.48E-06 2.59E-06 mr1911_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
vg0222743406 6.72E-07 4.77E-08 mr1918_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
vg0222743406 6.15E-08 8.50E-09 mr1929_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