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Detailed information for vg0433760044:

Variant ID: vg0433760044 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 33760044
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAAATATGTTTGACCGTTCGTCTTATTCAAAAACTTTTGTAAAATGTGTAAAACTATATGTATACATAAAAGTATATTTAACAATAAATCAAATGAGAG[G/A]
AAAAGAATTAACAATTATTTAAATTTTTTAAATAAGACGAACGATCAAATATTTTTAAAAAAGTCAACGACGTCAAACATTTTGGGATGGAGGTAGTACT

Reverse complement sequence

AGTACTACCTCCATCCCAAAATGTTTGACGTCGTTGACTTTTTTAAAAATATTTGATCGTTCGTCTTATTTAAAAAATTTAAATAATTGTTAATTCTTTT[C/T]
CTCTCATTTGATTTATTGTTAAATATACTTTTATGTATACATATAGTTTTACACATTTTACAAAAGTTTTTGAATAAGACGAACGGTCAAACATATTTAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.50%	31.50%	0.02%	0.00%	NA
All Indica	2759	98.40%	1.60%	0.04%	0.00%	NA
All Japonica	1512	18.10%	81.90%	0.00%	0.00%	NA
Aus	269	57.20%	42.80%	0.00%	0.00%	NA
Indica I	595	97.80%	2.20%	0.00%	0.00%	NA
Indica II	465	98.50%	1.50%	0.00%	0.00%	NA
Indica III	913	99.60%	0.30%	0.11%	0.00%	NA
Indica Intermediate	786	97.30%	2.70%	0.00%	0.00%	NA
Temperate Japonica	767	1.00%	99.00%	0.00%	0.00%	NA
Tropical Japonica	504	49.00%	51.00%	0.00%	0.00%	NA
Japonica Intermediate	241	7.50%	92.50%	0.00%	0.00%	NA
VI/Aromatic	96	49.00%	51.00%	0.00%	0.00%	NA
Intermediate	90	53.30%	46.70%	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
vg0433760044	G -> A	LOC_Os04g56620.1	upstream_gene_variant ; 1334.0bp to feature; MODIFIER	silent_mutation	Average:86.162; most accessible tissue: Callus, score: 96.551	N	N	N	N
vg0433760044	G -> A	LOC_Os04g56620.2	upstream_gene_variant ; 1334.0bp to feature; MODIFIER	silent_mutation	Average:86.162; most accessible tissue: Callus, score: 96.551	N	N	N	N
vg0433760044	G -> A	LOC_Os04g56600.1	downstream_gene_variant ; 4738.0bp to feature; MODIFIER	silent_mutation	Average:86.162; most accessible tissue: Callus, score: 96.551	N	N	N	N
vg0433760044	G -> A	LOC_Os04g56610.1	downstream_gene_variant ; 4171.0bp to feature; MODIFIER	silent_mutation	Average:86.162; most accessible tissue: Callus, score: 96.551	N	N	N	N
vg0433760044	G -> A	LOC_Os04g56630.1	downstream_gene_variant ; 4929.0bp to feature; MODIFIER	silent_mutation	Average:86.162; most accessible tissue: Callus, score: 96.551	N	N	N	N
vg0433760044	G -> A	LOC_Os04g56610-LOC_Os04g56620	intergenic_region ; MODIFIER	silent_mutation	Average:86.162; most accessible tissue: Callus, score: 96.551	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)
vg0433760044	G	A	-0.02	-0.01	-0.01	0.0	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0433760044	NA	1.01E-09	mr1248	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
vg0433760044	NA	1.67E-08	mr1946	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
vg0433760044	1.36E-08	NA	mr1188_2	Jap_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
vg0433760044	NA	1.46E-08	mr1805_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