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Detailed information for vg0920759077:

Variant ID: vg0920759077 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 20759077
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGACATGCGGTCTTGTTCACAGCTAGGGGTGGAAAAAAAAACTCAGGCTTGTGAGCTCAGCTCAGGCTTGGCTCGAGCTTGGTTGGCTCGGCTCGGCTC[G/A]
TAAACCAAACGAGCCAAGCCCAAGCCTCCTTTTCAGCTCGTTGCTGAAATGAGCCGAGCCGAGCTAGCTCGCTAGCCGCTTGTTTTGGCTCGCGAGCCTA

Reverse complement sequence

TAGGCTCGCGAGCCAAAACAAGCGGCTAGCGAGCTAGCTCGGCTCGGCTCATTTCAGCAACGAGCTGAAAAGGAGGCTTGGGCTTGGCTCGTTTGGTTTA[C/T]
GAGCCGAGCCGAGCCAACCAAGCTCGAGCCAAGCCTGAGCTGAGCTCACAAGCCTGAGTTTTTTTTTCCACCCCTAGCTGTGAACAAGACCGCATGTCCG

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	86.10%	13.30%	0.59%	0.00%	NA
All Indica	2759	99.20%	0.80%	0.04%	0.00%	NA
All Japonica	1512	59.90%	38.40%	1.72%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	98.30%	1.50%	0.13%	0.00%	NA
Temperate Japonica	767	85.40%	12.80%	1.83%	0.00%	NA
Tropical Japonica	504	13.50%	86.10%	0.40%	0.00%	NA
Japonica Intermediate	241	75.90%	19.90%	4.15%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	75.60%	23.30%	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
vg0920759077	G -> A	LOC_Os09g36040.1	downstream_gene_variant ; 4428.0bp to feature; MODIFIER	silent_mutation	Average:98.089; most accessible tissue: Zhenshan97 young leaf, score: 99.712	N	N	N	N
vg0920759077	G -> A	LOC_Os09g36050.1	downstream_gene_variant ; 1697.0bp to feature; MODIFIER	silent_mutation	Average:98.089; most accessible tissue: Zhenshan97 young leaf, score: 99.712	N	N	N	N
vg0920759077	G -> A	LOC_Os09g36050-LOC_Os09g36060	intergenic_region ; MODIFIER	silent_mutation	Average:98.089; most accessible tissue: Zhenshan97 young leaf, score: 99.712	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)
vg0920759077	G	A	-0.07	-0.07	-0.08	-0.06	-0.07	-0.07

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0920759077	NA	4.47E-06	mr1118	Jap_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
vg0920759077	NA	3.02E-11	mr1554	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
vg0920759077	NA	1.38E-09	mr1580	Jap_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
vg0920759077	NA	8.99E-06	mr1991	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
vg0920759077	NA	3.00E-12	mr1097_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
vg0920759077	NA	7.69E-09	mr1388_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
vg0920759077	NA	3.21E-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
vg0920759077	NA	6.50E-07	mr1554_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
vg0920759077	NA	1.05E-30	mr1699_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