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Detailed information for vg0601563713:

Variant ID: vg0601563713 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 1563713
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACTTCCCCTAGTAAAGCGGATTCAAGATCATGTTGGTAAAGTGCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTAC[G/A]
ACCTTGGGCCAATTGGCACTCTCAGGTTGTCTAGTCTAAACTCTCAATCGCCATTGAAGACGGTCGCACTAGTCAGTATCGGTACCACTCAGCAAAGGCA

Reverse complement sequence

TGCCTTTGCTGAGTGGTACCGATACTGACTAGTGCGACCGTCTTCAATGGCGATTGAGAGTTTAGACTAGACAACCTGAGAGTGCCAATTGGCCCAAGGT[C/T]
GTAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCACTTTACCAACATGATCTTGAATCCGCTTTACTAGGGGAAGTT

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	91.20%	6.50%	0.04%	2.26%	NA
All Indica	2759	94.70%	1.70%	0.07%	3.48%	NA
All Japonica	1512	87.00%	13.00%	0.00%	0.00%	NA
Aus	269	97.40%	0.40%	0.00%	2.23%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	81.90%	6.00%	0.43%	11.61%	NA
Indica III	913	99.10%	0.30%	0.00%	0.55%	NA
Indica Intermediate	786	93.10%	2.20%	0.00%	4.71%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	68.10%	31.90%	0.00%	0.00%	NA
Japonica Intermediate	241	85.90%	14.10%	0.00%	0.00%	NA
VI/Aromatic	96	54.20%	45.80%	0.00%	0.00%	NA
Intermediate	90	75.60%	18.90%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0601563713	G -> A	LOC_Os06g03890.1	upstream_gene_variant ; 1864.0bp to feature; MODIFIER	silent_mutation	Average:84.14; most accessible tissue: Minghui63 young leaf, score: 92.775	N	N	N	N
vg0601563713	G -> A	LOC_Os06g03860.1	downstream_gene_variant ; 2550.0bp to feature; MODIFIER	silent_mutation	Average:84.14; most accessible tissue: Minghui63 young leaf, score: 92.775	N	N	N	N
vg0601563713	G -> A	LOC_Os06g03880.1	downstream_gene_variant ; 1197.0bp to feature; MODIFIER	silent_mutation	Average:84.14; most accessible tissue: Minghui63 young leaf, score: 92.775	N	N	N	N
vg0601563713	G -> A	LOC_Os06g03860.4	downstream_gene_variant ; 3987.0bp to feature; MODIFIER	silent_mutation	Average:84.14; most accessible tissue: Minghui63 young leaf, score: 92.775	N	N	N	N
vg0601563713	G -> A	LOC_Os06g03860.2	downstream_gene_variant ; 2550.0bp to feature; MODIFIER	silent_mutation	Average:84.14; most accessible tissue: Minghui63 young leaf, score: 92.775	N	N	N	N
vg0601563713	G -> A	LOC_Os06g03860.3	downstream_gene_variant ; 2550.0bp to feature; MODIFIER	silent_mutation	Average:84.14; most accessible tissue: Minghui63 young leaf, score: 92.775	N	N	N	N
vg0601563713	G -> A	LOC_Os06g03860-LOC_Os06g03880	intergenic_region ; MODIFIER	silent_mutation	Average:84.14; most accessible tissue: Minghui63 young leaf, score: 92.775	N	N	N	N
vg0601563713	G -> DEL	N	N	silent_mutation	Average:84.14; most accessible tissue: Minghui63 young leaf, score: 92.775	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)
vg0601563713	G	A	0.03	0.02	0.02	0.03	0.04	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0601563713	2.63E-06	NA	mr1040_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
vg0601563713	2.11E-06	NA	mr1070_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
vg0601563713	8.74E-06	NA	mr1107_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
vg0601563713	9.58E-06	NA	mr1155_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
vg0601563713	3.88E-06	NA	mr1208_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
vg0601563713	NA	4.65E-08	mr1304_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
vg0601563713	2.31E-06	2.31E-06	mr1367_2	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
vg0601563713	NA	4.37E-08	mr1408_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
vg0601563713	4.26E-06	NA	mr1606_2	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
vg0601563713	6.03E-07	NA	mr1846_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
vg0601563713	9.51E-06	9.51E-06	mr1846_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
vg0601563713	NA	2.50E-06	mr1852_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