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Detailed information for vg0427543202:

Variant ID: vg0427543202 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 27543202
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

GCAGCCCGTTTGTTGCCTGGCTGGTGTACATTAGGCAGGTCTTGGTTGGATCCAAAAAATTTTGGTTAAAAATATAAAATTAAATGTTTAGACATTAAAT[G/A]
TTTAGACATATGTATGATTTATTAAATATGAAAAAAAAATCAATTACGCAATTTGCATGTAAATTACGAGACGAATTTTTTAAGTCTAATTACGTTATAA

Reverse complement sequence

TTATAACGTAATTAGACTTAAAAAATTCGTCTCGTAATTTACATGCAAATTGCGTAATTGATTTTTTTTTCATATTTAATAAATCATACATATGTCTAAA[C/T]
ATTTAATGTCTAAACATTTAATTTTATATTTTTAACCAAAATTTTTTGGATCCAACCAAGACCTGCCTAATGTACACCAGCCAGGCAACAAACGGGCTGC

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	65.40%	33.90%	0.32%	0.38%	NA
All Indica	2759	41.70%	57.30%	0.47%	0.58%	NA
All Japonica	1512	99.80%	0.10%	0.07%	0.00%	NA
Aus	269	98.10%	1.50%	0.37%	0.00%	NA
Indica I	595	19.70%	79.80%	0.17%	0.34%	NA
Indica II	465	79.60%	20.20%	0.00%	0.22%	NA
Indica III	913	32.40%	66.70%	0.33%	0.55%	NA
Indica Intermediate	786	46.70%	51.10%	1.15%	1.02%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	78.90%	18.90%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0427543202	G -> DEL	N	N	silent_mutation	Average:94.635; most accessible tissue: Callus, score: 99.421	N	N	N	N
vg0427543202	G -> A	LOC_Os04g46444.1	upstream_gene_variant ; 1214.0bp to feature; MODIFIER	silent_mutation	Average:94.635; most accessible tissue: Callus, score: 99.421	N	N	N	N
vg0427543202	G -> A	LOC_Os04g46440.1	downstream_gene_variant ; 2273.0bp to feature; MODIFIER	silent_mutation	Average:94.635; most accessible tissue: Callus, score: 99.421	N	N	N	N
vg0427543202	G -> A	LOC_Os04g46440-LOC_Os04g46444	intergenic_region ; MODIFIER	silent_mutation	Average:94.635; most accessible tissue: Callus, score: 99.421	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)
vg0427543202	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
vg0427543202	NA	1.36E-06	mr1174	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
vg0427543202	NA	2.30E-07	mr1298	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
vg0427543202	NA	8.06E-09	mr1731	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
vg0427543202	NA	1.70E-08	mr1174_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
vg0427543202	NA	1.15E-07	mr1347_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
vg0427543202	NA	5.19E-07	mr1355_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
vg0427543202	NA	8.09E-06	mr1355_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
vg0427543202	NA	6.41E-07	mr1539_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
vg0427543202	NA	1.16E-06	mr1540_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
vg0427543202	NA	5.47E-07	mr1732_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
vg0427543202	NA	2.68E-06	mr1899_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
vg0427543202	NA	3.96E-06	mr1910_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
vg0427543202	NA	1.83E-06	mr1923_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
vg0427543202	NA	3.14E-06	mr1923_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