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Detailed information for vg0224508221:

Variant ID: vg0224508221 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24508221
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: 122. )

Flanking Sequence (100 bp) in Reference Genome:

AAAAAAAAAAGAAAAGAGGACGGGCCGAATGATTTTAATTCTCAGCCAACTTGGGCCTGTAACGATCTAGCCCATCACGACCCATTCGGTTAAAACACCT[G/A]
GGTAATAACGATAATGCTTGTCGCCGGGCGACCGGCGCGGGGGGAGCCGGATCAAGCACTCCCCCCACGCGCGCCTCTCCCCCACGTGCTACCTGTTGTC

Reverse complement sequence

GACAACAGGTAGCACGTGGGGGAGAGGCGCGCGTGGGGGGAGTGCTTGATCCGGCTCCCCCCGCGCCGGTCGCCCGGCGACAAGCATTATCGTTATTACC[C/T]
AGGTGTTTTAACCGAATGGGTCGTGATGGGCTAGATCGTTACAGGCCCAAGTTGGCTGAGAATTAAAATCATTCGGCCCGTCCTCTTTTCTTTTTTTTTT

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	93.40%	5.30%	1.31%	0.00%	NA
All Indica	2759	92.00%	7.80%	0.29%	0.00%	NA
All Japonica	1512	95.80%	0.70%	3.44%	0.00%	NA
Aus	269	91.80%	8.20%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	83.40%	16.60%	0.00%	0.00%	NA
Indica III	913	93.00%	6.70%	0.33%	0.00%	NA
Indica Intermediate	786	89.80%	9.50%	0.64%	0.00%	NA
Temperate Japonica	767	97.90%	0.10%	1.96%	0.00%	NA
Tropical Japonica	504	93.70%	1.60%	4.76%	0.00%	NA
Japonica Intermediate	241	93.80%	0.80%	5.39%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	2.20%	2.22%	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
vg0224508221	G -> A	LOC_Os02g40430-LOC_Os02g40440	intergenic_region ; MODIFIER	silent_mutation	Average:92.255; most accessible tissue: Callus, score: 98.591	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)
vg0224508221	G	A	-0.16	-0.16	-0.14	-0.12	-0.1	-0.11

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224508221	NA	2.05E-06	mr1074	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
vg0224508221	4.90E-06	NA	mr1072_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
vg0224508221	3.31E-06	2.11E-09	mr1072_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
vg0224508221	6.89E-06	1.18E-08	mr1075_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
vg0224508221	NA	4.27E-09	mr1077_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
vg0224508221	9.02E-06	1.48E-08	mr1149_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
vg0224508221	NA	1.38E-06	mr1406_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
vg0224508221	NA	8.14E-08	mr1406_2	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
vg0224508221	NA	6.65E-06	mr1592_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
vg0224508221	NA	3.79E-06	mr1767_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