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Detailed information for vg0427823476:

Variant ID: vg0427823476 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 27823476
Reference Allele: G	Alternative Allele: A,T
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTGAAAAAGGCAAATCAGGGATCTTTTTGTAAAATTCGCGTCAAGCGATCTTTTTAGATAATTCAAAAAAAAAAAAAAAAATGGATTACATCGATTCT[G/A,T]
CCATAAGACATACTTCCTCCGTTTCACAATGTAAATCATTCTAGCATTTCCCACATTCGTATCGATGCTAATGAATCCAAGACATATATATGTCTTAGAT

Reverse complement sequence

ATCTAAGACATATATATGTCTTGGATTCATTAGCATCGATACGAATGTGGGAAATGCTAGAATGATTTACATTGTGAAACGGAGGAAGTATGTCTTATGG[C/T,A]
AGAATCGATGTAATCCATTTTTTTTTTTTTTTTTGAATTATCTAAAAAGATCGCTTGACGCGAATTTTACAAAAAGATCCCTGATTTGCCTTTTTCAGAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	82.10%	17.80%	0.04%	0.00%	T: 0.02%
All Indica	2759	75.50%	24.50%	0.07%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	43.50%	56.10%	0.00%	0.00%	T: 0.37%
Indica I	595	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	31.20%	68.80%	0.00%	0.00%	NA
Indica III	913	85.90%	14.10%	0.00%	0.00%	NA
Indica Intermediate	786	71.50%	28.20%	0.25%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	0.00%	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
vg0427823476	G -> A	LOC_Os04g46910.1	upstream_gene_variant ; 3342.0bp to feature; MODIFIER	silent_mutation	Average:91.026; most accessible tissue: Callus, score: 96.062	N	N	N	N
vg0427823476	G -> A	LOC_Os04g46920.1	upstream_gene_variant ; 238.0bp to feature; MODIFIER	silent_mutation	Average:91.026; most accessible tissue: Callus, score: 96.062	N	N	N	N
vg0427823476	G -> A	LOC_Os04g46920.2	upstream_gene_variant ; 238.0bp to feature; MODIFIER	silent_mutation	Average:91.026; most accessible tissue: Callus, score: 96.062	N	N	N	N
vg0427823476	G -> A	LOC_Os04g46930.1	downstream_gene_variant ; 339.0bp to feature; MODIFIER	silent_mutation	Average:91.026; most accessible tissue: Callus, score: 96.062	N	N	N	N
vg0427823476	G -> A	LOC_Os04g46930.2	downstream_gene_variant ; 339.0bp to feature; MODIFIER	silent_mutation	Average:91.026; most accessible tissue: Callus, score: 96.062	N	N	N	N
vg0427823476	G -> A	LOC_Os04g46920-LOC_Os04g46930	intergenic_region ; MODIFIER	silent_mutation	Average:91.026; most accessible tissue: Callus, score: 96.062	N	N	N	N
vg0427823476	G -> T	LOC_Os04g46910.1	upstream_gene_variant ; 3342.0bp to feature; MODIFIER	silent_mutation	Average:91.026; most accessible tissue: Callus, score: 96.062	N	N	N	N
vg0427823476	G -> T	LOC_Os04g46920.1	upstream_gene_variant ; 238.0bp to feature; MODIFIER	silent_mutation	Average:91.026; most accessible tissue: Callus, score: 96.062	N	N	N	N
vg0427823476	G -> T	LOC_Os04g46920.2	upstream_gene_variant ; 238.0bp to feature; MODIFIER	silent_mutation	Average:91.026; most accessible tissue: Callus, score: 96.062	N	N	N	N
vg0427823476	G -> T	LOC_Os04g46930.1	downstream_gene_variant ; 339.0bp to feature; MODIFIER	silent_mutation	Average:91.026; most accessible tissue: Callus, score: 96.062	N	N	N	N
vg0427823476	G -> T	LOC_Os04g46930.2	downstream_gene_variant ; 339.0bp to feature; MODIFIER	silent_mutation	Average:91.026; most accessible tissue: Callus, score: 96.062	N	N	N	N
vg0427823476	G -> T	LOC_Os04g46920-LOC_Os04g46930	intergenic_region ; MODIFIER	silent_mutation	Average:91.026; most accessible tissue: Callus, score: 96.062	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)
vg0427823476	G	A	-0.04	-0.06	-0.05	-0.03	-0.04	-0.04
vg0427823476	G	T	-0.03	-0.04	-0.03	-0.04	-0.03	-0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0427823476	NA	4.84E-06	mr1013	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
vg0427823476	NA	1.81E-06	mr1031	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
vg0427823476	NA	5.36E-07	mr1050	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
vg0427823476	NA	7.00E-06	mr1163	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
vg0427823476	NA	5.12E-08	mr1174	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
vg0427823476	NA	1.11E-07	mr1174	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
vg0427823476	NA	1.18E-06	mr1354	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
vg0427823476	NA	6.02E-06	mr1626	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
vg0427823476	NA	1.17E-06	mr1709	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
vg0427823476	NA	4.01E-06	mr1798	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
vg0427823476	1.90E-06	1.90E-06	mr1035_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
vg0427823476	NA	8.15E-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
vg0427823476	NA	2.01E-06	mr1158_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
vg0427823476	NA	4.43E-08	mr1170_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
vg0427823476	5.69E-06	NA	mr1242_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
vg0427823476	NA	5.51E-06	mr1272_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
vg0427823476	NA	5.15E-08	mr1354_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
vg0427823476	NA	7.09E-06	mr1355_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
vg0427823476	NA	3.27E-06	mr1439_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
vg0427823476	NA	3.04E-08	mr1449_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
vg0427823476	NA	3.18E-06	mr1449_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
vg0427823476	NA	3.17E-07	mr1458_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
vg0427823476	NA	1.20E-06	mr1478_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
vg0427823476	NA	3.97E-07	mr1631_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
vg0427823476	NA	2.75E-11	mr1715_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
vg0427823476	NA	6.20E-06	mr1719_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
vg0427823476	NA	9.43E-08	mr1720_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
vg0427823476	NA	3.18E-06	mr1733_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
vg0427823476	NA	4.29E-08	mr1895_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
vg0427823476	NA	1.79E-07	mr1904_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
vg0427823476	NA	1.53E-06	mr1931_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
vg0427823476	NA	4.82E-07	mr1931_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
vg0427823476	NA	5.82E-07	mr1942_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