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Detailed information for vg0300733892:

Variant ID: vg0300733892 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 733892
Reference Allele: GAlternative Allele: A,C
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


TGTGGGGGTGGCGGACGCGGAGGAGGGCGTCGAGCTCCTGGCGGAAGGCGCGCTGGAGGCGCTCGCTGCTGCGGTGGACCTTGACGGCCGCGAGGGAGCC[G/A,C]
GCGACGCGGCCGAGGTAGACGGTGCTGAAGCCGCCCTCGCCGACGACGGCCGACGTGAACCCACGCGTCATGGCCTCCACCTGCGCCCACGACAGCTGCC

Reverse complement sequence

GGCAGCTGTCGTGGGCGCAGGTGGAGGCCATGACGCGTGGGTTCACGTCGGCCGTCGTCGGCGAGGGCGGCTTCAGCACCGTCTACCTCGGCCGCGTCGC[C/T,G]
GGCTCCCTCGCGGCCGTCAAGGTCCACCGCAGCAGCGAGCGCCTCCAGCGCGCCTTCCGCCAGGAGCTCGACGCCCTCCTCCGCGTCCGCCACCCCCACA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.60% 44.10% 1.02% 0.28% NA
All Indica  2759 86.20% 13.50% 0.22% 0.04% NA
All Japonica  1512 0.70% 96.10% 2.38% 0.79% NA
Aus  269 50.20% 49.10% 0.74% 0.00% NA
Indica I  595 98.20% 1.80% 0.00% 0.00% NA
Indica II  465 61.30% 38.30% 0.22% 0.22% NA
Indica III  913 94.10% 5.60% 0.33% 0.00% NA
Indica Intermediate  786 82.80% 16.90% 0.25% 0.00% NA
Temperate Japonica  767 0.40% 93.70% 4.30% 1.56% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 97.50% 1.24% 0.00% NA
VI/Aromatic  96 15.60% 81.20% 3.12% 0.00% NA
Intermediate  90 43.30% 55.60% 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
vg0300733892 G -> C LOC_Os03g02190.1 synonymous_variant ; p.Ala82Ala; LOW N Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0300733892 G -> C LOC_Os03g02200.1 upstream_gene_variant ; 2291.0bp to feature; MODIFIER N Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0300733892 G -> C LOC_Os03g02200.2 upstream_gene_variant ; 2291.0bp to feature; MODIFIER N Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0300733892 G -> C LOC_Os03g02200.3 upstream_gene_variant ; 2291.0bp to feature; MODIFIER N Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0300733892 G -> A LOC_Os03g02190.1 synonymous_variant ; p.Ala82Ala; LOW synonymous_codon Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0300733892 G -> DEL LOC_Os03g02190.1 N frameshift_variant Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 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)
vg0300733892 G A 0.0 -0.01 -0.01 -0.01 0.01 0.0
vg0300733892 G C 0.02 0.0 0.02 -0.01 0.03 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0300733892 NA 4.91E-09 mr1317 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
vg0300733892 NA 2.17E-07 mr1317 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
vg0300733892 NA 3.42E-06 mr1607 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
vg0300733892 NA 5.47E-09 mr1644 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
vg0300733892 NA 1.80E-08 mr1818 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
vg0300733892 NA 6.95E-11 mr1855 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
vg0300733892 NA 1.98E-07 mr1877 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
vg0300733892 NA 1.18E-09 mr1050_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
vg0300733892 NA 2.05E-06 mr1050_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
vg0300733892 NA 2.30E-14 mr1191_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
vg0300733892 NA 2.40E-06 mr1272_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
vg0300733892 NA 4.68E-08 mr1317_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
vg0300733892 NA 9.61E-08 mr1321_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
vg0300733892 NA 1.39E-06 mr1428_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
vg0300733892 NA 3.18E-08 mr1446_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
vg0300733892 NA 6.76E-07 mr1855_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
vg0300733892 NA 1.84E-06 mr1875_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
vg0300733892 NA 4.48E-07 mr1914_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
vg0300733892 NA 7.15E-09 mr1946_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
vg0300733892 NA 7.15E-09 mr1948_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