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Detailed information for vg0122959545:

Variant ID: vg0122959545 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 22959545
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.07, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

CACACGTTTGGGAATAGGGGTGAAAACGGATATTTTTTAAAAAAACGGGTGCGGATGCGGAGCGTGTTTCGAATATCGGAAATGGGTGCGGAGCGGTGCG[G/A]
ACTTGGTTCGGAAAAGGATTAAAATTATTGGATGTTATGTATATATACAAGGGACGATATTGATTTAGCAATACAGGGGACAACAATAACGACTCATAAG

Reverse complement sequence

CTTATGAGTCGTTATTGTTGTCCCCTGTATTGCTAAATCAATATCGTCCCTTGTATATATACATAACATCCAATAATTTTAATCCTTTTCCGAACCAAGT[C/T]
CGCACCGCTCCGCACCCATTTCCGATATTCGAAACACGCTCCGCATCCGCACCCGTTTTTTTAAAAAATATCCGTTTTCACCCCTATTCCCAAACGTGTG

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	75.10%	24.80%	0.11%	0.00%	NA
All Indica	2759	83.40%	16.40%	0.18%	0.00%	NA
All Japonica	1512	62.40%	37.60%	0.00%	0.00%	NA
Aus	269	58.40%	41.60%	0.00%	0.00%	NA
Indica I	595	98.00%	2.00%	0.00%	0.00%	NA
Indica II	465	66.70%	33.10%	0.22%	0.00%	NA
Indica III	913	87.70%	12.20%	0.11%	0.00%	NA
Indica Intermediate	786	77.20%	22.40%	0.38%	0.00%	NA
Temperate Japonica	767	95.70%	4.30%	0.00%	0.00%	NA
Tropical Japonica	504	18.30%	81.70%	0.00%	0.00%	NA
Japonica Intermediate	241	48.50%	51.50%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	61.10%	38.90%	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
vg0122959545	G -> A	LOC_Os01g40630.1	upstream_gene_variant ; 320.0bp to feature; MODIFIER	silent_mutation	Average:95.136; most accessible tissue: Minghui63 flag leaf, score: 99.161	N	N	N	N
vg0122959545	G -> A	LOC_Os01g40630.3	upstream_gene_variant ; 2275.0bp to feature; MODIFIER	silent_mutation	Average:95.136; most accessible tissue: Minghui63 flag leaf, score: 99.161	N	N	N	N
vg0122959545	G -> A	LOC_Os01g40630.2	upstream_gene_variant ; 400.0bp to feature; MODIFIER	silent_mutation	Average:95.136; most accessible tissue: Minghui63 flag leaf, score: 99.161	N	N	N	N
vg0122959545	G -> A	LOC_Os01g40630-LOC_Os01g40640	intergenic_region ; MODIFIER	silent_mutation	Average:95.136; most accessible tissue: Minghui63 flag leaf, score: 99.161	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)
vg0122959545	G	A	-0.09	-0.07	-0.09	-0.1	-0.11	-0.1

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0122959545	NA	4.05E-07	mr1346	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
vg0122959545	3.40E-06	3.15E-07	mr1587	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
vg0122959545	NA	1.33E-07	mr1861	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
vg0122959545	NA	2.06E-06	mr1936	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
vg0122959545	NA	5.34E-08	mr1962	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
vg0122959545	NA	5.17E-09	mr1072_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
vg0122959545	NA	1.21E-08	mr1075_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
vg0122959545	NA	1.47E-08	mr1124_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
vg0122959545	NA	1.14E-08	mr1149_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
vg0122959545	7.16E-06	9.70E-09	mr1346_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
vg0122959545	NA	3.28E-06	mr1346_2	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
vg0122959545	NA	5.59E-09	mr1441_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
vg0122959545	NA	2.63E-06	mr1456_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
vg0122959545	NA	3.92E-07	mr1795_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