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Detailed information for vg0137934842:

Variant ID: vg0137934842 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 37934842
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

GATATATTTATATTTTTATGAAAGTATTTTTCAAGACAAATCTATACATATAATTTTTACATTTTCAAACTCAACAGCTTGAGAGTTATTTATGATTTAT[A/G]
TTCCCAAGGTTCGACTTAAACATTGTGATAAACGATTTTTTTTATGAGTACGGAGGGAGTATTTCTAAAATAAACAATTAAAATCGGGTATAGGTTGGTC

Reverse complement sequence

GACCAACCTATACCCGATTTTAATTGTTTATTTTAGAAATACTCCCTCCGTACTCATAAAAAAAATCGTTTATCACAATGTTTAAGTCGAACCTTGGGAA[T/C]
ATAAATCATAAATAACTCTCAAGCTGTTGAGTTTGAAAATGTAAAAATTATATGTATAGATTTGTCTTGAAAAATACTTTCATAAAAATATAAATATATC

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	76.50%	23.20%	0.34%	0.00%	NA
All Indica	2759	67.60%	31.90%	0.54%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	27.10%	72.50%	0.37%	0.00%	NA
Indica I	595	63.90%	35.60%	0.50%	0.00%	NA
Indica II	465	85.80%	14.00%	0.22%	0.00%	NA
Indica III	913	54.80%	44.90%	0.33%	0.00%	NA
Indica Intermediate	786	74.60%	24.40%	1.02%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	14.40%	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
vg0137934842	A -> G	LOC_Os01g65370.1	downstream_gene_variant ; 1547.0bp to feature; MODIFIER	silent_mutation	Average:57.414; most accessible tissue: Minghui63 flower, score: 84.168	N	N	N	N
vg0137934842	A -> G	LOC_Os01g65370-LOC_Os01g65380	intergenic_region ; MODIFIER	silent_mutation	Average:57.414; most accessible tissue: Minghui63 flower, score: 84.168	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)
vg0137934842	A	G	-0.02	-0.03	-0.02	-0.02	-0.01	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0137934842	1.21E-06	NA	mr1134	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
vg0137934842	1.78E-07	NA	mr1517	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
vg0137934842	5.47E-13	8.27E-15	mr1517	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
vg0137934842	2.26E-07	NA	mr1538	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
vg0137934842	8.59E-11	6.39E-12	mr1538	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
vg0137934842	4.77E-06	NA	mr1134_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
vg0137934842	4.85E-06	9.25E-07	mr1134_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
vg0137934842	1.91E-08	NA	mr1517_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
vg0137934842	3.49E-14	1.10E-13	mr1517_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
vg0137934842	2.31E-06	NA	mr1538_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
vg0137934842	1.25E-10	1.71E-13	mr1538_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