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Detailed information for vg0501597981:

Variant ID: vg0501597981 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 1597981
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

GCCAACCACTCCGGATGGATAACCTCGCGGATAAAGTCAGCCTCCAGGAGCCGCGCCACTTCCTCTCGGATGAAGGCCTGCCGCTCCGGGGCTTGACACC[G/A]
CACTTTTTGCCGGACGGGTCGCGCATCCAGCCGCATGGCGAGGCGGTGCTCGATCACCTCCCTAGGGACCCCGGGCATGTCCGACGGCTTCCATTCGAAG

Reverse complement sequence

CTTCGAATGGAAGCCGTCGGACATGCCCGGGGTCCCTAGGGAGGTGATCGAGCACCGCCTCGCCATGCGGCTGGATGCGCGACCCGTCCGGCAAAAAGTG[C/T]
GGTGTCAAGCCCCGGAGCGGCAGGCCTTCATCCGAGAGGAAGTGGCGCGGCTCCTGGAGGCTGACTTTATCCGCGAGGTTATCCATCCGGAGTGGTTGGC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.70%	47.10%	2.20%	0.00%	NA
All Indica	2759	85.10%	11.20%	3.73%	0.00%	NA
All Japonica	1512	1.10%	98.90%	0.00%	0.00%	NA
Aus	269	1.50%	98.50%	0.00%	0.00%	NA
Indica I	595	94.50%	4.00%	1.51%	0.00%	NA
Indica II	465	82.20%	11.40%	6.45%	0.00%	NA
Indica III	913	80.30%	16.10%	3.61%	0.00%	NA
Indica Intermediate	786	85.40%	10.70%	3.94%	0.00%	NA
Temperate Japonica	767	0.90%	99.10%	0.00%	0.00%	NA
Tropical Japonica	504	1.00%	99.00%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	0.00%	100.00%	0.00%	0.00%	NA
Intermediate	90	31.10%	67.80%	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
vg0501597981	G -> A	LOC_Os05g03670.1	upstream_gene_variant ; 1888.0bp to feature; MODIFIER	silent_mutation	Average:47.526; most accessible tissue: Zhenshan97 flag leaf, score: 73.822	N	N	N	N
vg0501597981	G -> A	LOC_Os05g03680.1	downstream_gene_variant ; 142.0bp to feature; MODIFIER	silent_mutation	Average:47.526; most accessible tissue: Zhenshan97 flag leaf, score: 73.822	N	N	N	N
vg0501597981	G -> A	LOC_Os05g03670-LOC_Os05g03680	intergenic_region ; MODIFIER	silent_mutation	Average:47.526; most accessible tissue: Zhenshan97 flag leaf, score: 73.822	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)
vg0501597981	G	A	-0.01	-0.01	-0.01	-0.01	-0.01	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0501597981	NA	3.24E-06	mr1029	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
vg0501597981	NA	5.98E-10	mr1047	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
vg0501597981	NA	1.35E-15	mr1164	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
vg0501597981	9.67E-07	9.67E-07	mr1184	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
vg0501597981	NA	1.57E-07	mr1189	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
vg0501597981	NA	4.15E-08	mr1260	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
vg0501597981	NA	1.00E-15	mr1261	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
vg0501597981	NA	2.10E-06	mr1334	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
vg0501597981	NA	7.88E-07	mr1625	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
vg0501597981	NA	6.18E-07	mr1734	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
vg0501597981	NA	5.98E-12	mr1744	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
vg0501597981	NA	8.16E-06	mr1750	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
vg0501597981	NA	9.47E-26	mr1051_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
vg0501597981	NA	5.13E-29	mr1932_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