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Detailed information for vg0203470483:

Variant ID: vg0203470483 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 3470483
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATTTCGTTGTTAGATTTTTTTTTTGTCAGGACGGACGGAAGGGAGTATGTTTGATGTGACCTTCTATTCCATCCCAGAAAAAAACAAATTTGAGCTAT[G/A]
AACCTGGACACACATATGTTAACCTATTGATCCAAACACATGTTTATCGTGGAGTGCCACAGCCTCCCTCGCGGCGCACGGACGCGGCCTCCTCGTGTCT

Reverse complement sequence

AGACACGAGGAGGCCGCGTCCGTGCGCCGCGAGGGAGGCTGTGGCACTCCACGATAAACATGTGTTTGGATCAATAGGTTAACATATGTGTGTCCAGGTT[C/T]
ATAGCTCAAATTTGTTTTTTTCTGGGATGGAATAGAAGGTCACATCAAACATACTCCCTTCCGTCCGTCCTGACAAAAAAAAAATCTAACAACGAAATAT

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	98.30%	1.10%	0.66%	0.00%	NA
All Indica	2759	99.10%	0.40%	0.51%	0.00%	NA
All Japonica	1512	96.40%	2.40%	1.12%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.50%	0.00%	0.50%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	97.60%	1.20%	1.20%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	99.00%	0.70%	0.39%	0.00%	NA
Tropical Japonica	504	92.90%	4.80%	2.38%	0.00%	NA
Japonica Intermediate	241	95.90%	3.30%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0203470483	G -> A	LOC_Os02g06890.1	upstream_gene_variant ; 51.0bp to feature; MODIFIER	silent_mutation	Average:94.632; most accessible tissue: Minghui63 young leaf, score: 96.742	N	N	N	N
vg0203470483	G -> A	LOC_Os02g06880.1	downstream_gene_variant ; 1404.0bp to feature; MODIFIER	silent_mutation	Average:94.632; most accessible tissue: Minghui63 young leaf, score: 96.742	N	N	N	N
vg0203470483	G -> A	LOC_Os02g06880-LOC_Os02g06890	intergenic_region ; MODIFIER	silent_mutation	Average:94.632; most accessible tissue: Minghui63 young leaf, score: 96.742	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)
vg0203470483	G	A	0.02	0.08	0.09	0.03	0.04	0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0203470483	NA	5.25E-07	mr1044	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
vg0203470483	4.82E-06	4.82E-06	mr1160	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
vg0203470483	5.89E-07	6.53E-08	mr1192	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
vg0203470483	NA	6.63E-06	mr1906	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
vg0203470483	NA	3.50E-06	mr1982	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
vg0203470483	1.98E-06	1.98E-06	mr1400_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
vg0203470483	1.22E-06	1.22E-06	mr1610_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