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Detailed information for vg0819873123:

Variant ID: vg0819873123 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 19873123
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGATTCGATGCCTTAGGTCCTCCCAGGGGTCCCTTTTATACCACAGGTCAACTGGTCTCCAAGTAGGACTCGGAGACATCGGACCCGATACGATACAAT[G/A]
ACGACCCAATTCTATCCGAGTAGGACTCCTTACATCTGTGAACTCCATAATGAATTTCCTTAACTTATGCCGAAAACGTCCGTATGTGCGCAAGTATACC

Reverse complement sequence

GGTATACTTGCGCACATACGGACGTTTTCGGCATAAGTTAAGGAAATTCATTATGGAGTTCACAGATGTAAGGAGTCCTACTCGGATAGAATTGGGTCGT[C/T]
ATTGTATCGTATCGGGTCCGATGTCTCCGAGTCCTACTTGGAGACCAGTTGACCTGTGGTATAAAAGGGACCCCTGGGAGGACCTAAGGCATCGAATCTT

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	85.90%	5.20%	3.64%	5.25%	NA
All Indica	2759	78.00%	7.80%	5.84%	8.45%	NA
All Japonica	1512	99.80%	0.10%	0.07%	0.07%	NA
Aus	269	89.20%	10.40%	0.00%	0.37%	NA
Indica I	595	81.70%	16.80%	0.17%	1.34%	NA
Indica II	465	92.90%	0.20%	3.01%	3.87%	NA
Indica III	913	70.00%	3.60%	12.38%	14.02%	NA
Indica Intermediate	786	75.60%	10.20%	4.20%	10.05%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	83.30%	0.00%	6.25%	10.42%	NA
Intermediate	90	88.90%	3.30%	4.44%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0819873123	G -> A	LOC_Os08g32030.1	upstream_gene_variant ; 3780.0bp to feature; MODIFIER	silent_mutation	Average:40.874; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg0819873123	G -> A	LOC_Os08g32040.1	upstream_gene_variant ; 2659.0bp to feature; MODIFIER	silent_mutation	Average:40.874; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg0819873123	G -> A	LOC_Os08g32050.1	upstream_gene_variant ; 589.0bp to feature; MODIFIER	silent_mutation	Average:40.874; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg0819873123	G -> A	LOC_Os08g32060.1	upstream_gene_variant ; 2143.0bp to feature; MODIFIER	silent_mutation	Average:40.874; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg0819873123	G -> A	LOC_Os08g32050-LOC_Os08g32060	intergenic_region ; MODIFIER	silent_mutation	Average:40.874; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg0819873123	G -> DEL	N	N	silent_mutation	Average:40.874; most accessible tissue: Zhenshan97 panicle, score: 82.888	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)
vg0819873123	G	A	0.0	-0.01	0.0	0.0	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0819873123	4.14E-06	1.09E-06	mr1755	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
vg0819873123	NA	1.32E-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
vg0819873123	NA	2.50E-06	mr1971	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
vg0819873123	NA	8.56E-06	mr1566_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
vg0819873123	NA	2.04E-06	mr1823_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
vg0819873123	NA	6.27E-06	mr1831_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
vg0819873123	NA	1.15E-06	mr1856_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
vg0819873123	NA	2.94E-06	mr1971_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