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Detailed information for vg0521968750:

Variant ID: vg0521968750 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 21968750
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGCCTTATTTTTTTTTGGAAGACTCCACCTGCTATATAGTACTCACTCCGTTTTGAAATGTTTAATACCGTTAACTTTTTAGCACATGTTTGACCGTTC[G/A]
TCTTATTCAAAAACTTTTGTGAAATATGTAAAATTATATGCCTACATCAAAATATATTTAACAATAAATCAAATGATAGGAAAAGAATTAATAATTACTT

Reverse complement sequence

AAGTAATTATTAATTCTTTTCCTATCATTTGATTTATTGTTAAATATATTTTGATGTAGGCATATAATTTTACATATTTCACAAAAGTTTTTGAATAAGA[C/T]
GAACGGTCAAACATGTGCTAAAAAGTTAACGGTATTAAACATTTCAAAACGGAGTGAGTACTATATAGCAGGTGGAGTCTTCCAAAAAAAAATAAGGCCT

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	60.20%	39.30%	0.23%	0.25%	NA
All Indica	2759	37.80%	61.50%	0.33%	0.40%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	56.50%	43.50%	0.00%	0.00%	NA
Indica I	595	54.10%	45.00%	0.34%	0.50%	NA
Indica II	465	15.10%	83.90%	0.86%	0.22%	NA
Indica III	913	42.60%	56.50%	0.22%	0.66%	NA
Indica Intermediate	786	33.20%	66.50%	0.13%	0.13%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	57.80%	38.90%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0521968750	G -> DEL	N	N	silent_mutation	Average:77.342; most accessible tissue: Minghui63 root, score: 91.021	N	N	N	N
vg0521968750	G -> A	LOC_Os05g37520.2	upstream_gene_variant ; 2738.0bp to feature; MODIFIER	silent_mutation	Average:77.342; most accessible tissue: Minghui63 root, score: 91.021	N	N	N	N
vg0521968750	G -> A	LOC_Os05g37530.1	upstream_gene_variant ; 1633.0bp to feature; MODIFIER	silent_mutation	Average:77.342; most accessible tissue: Minghui63 root, score: 91.021	N	N	N	N
vg0521968750	G -> A	LOC_Os05g37520.1	upstream_gene_variant ; 2738.0bp to feature; MODIFIER	silent_mutation	Average:77.342; most accessible tissue: Minghui63 root, score: 91.021	N	N	N	N
vg0521968750	G -> A	LOC_Os05g37520-LOC_Os05g37530	intergenic_region ; MODIFIER	silent_mutation	Average:77.342; most accessible tissue: Minghui63 root, score: 91.021	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)
vg0521968750	G	A	0.01	0.01	0.0	0.01	0.01	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0521968750	NA	3.91E-07	mr1044	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
vg0521968750	NA	3.83E-06	mr1115	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
vg0521968750	NA	4.53E-06	mr1195	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
vg0521968750	NA	3.92E-06	mr1304	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
vg0521968750	NA	3.18E-06	mr1352	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
vg0521968750	NA	9.59E-06	mr1407	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
vg0521968750	NA	6.49E-06	mr1624	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
vg0521968750	NA	2.93E-06	mr1735	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
vg0521968750	6.50E-06	4.70E-07	mr1737	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
vg0521968750	NA	3.54E-06	mr1788	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
vg0521968750	NA	2.69E-06	mr1832	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
vg0521968750	NA	7.06E-06	mr1992	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