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Detailed information for vg0224817087:

Variant ID: vg0224817087 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24817087
Reference Allele: C	Alternative Allele: A,T
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, A: 0.01, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

TACCAGGGGAGGGCGCCCAACGGCGTCAAGACCGGCTGGGTTATGCACGAGTTCCGCCTCGACTCCCCGCACTCCCAACCCAGGGTACGTACGTCATACA[C/A,T]
ATAAGCCGTGCGCCAACGCATTGAACTTATTTTGATCCTTATCACATTTTTTTATGTCCTCTACATAGATATAAGATTTGCTCCGATCCAATAAAAAATA

Reverse complement sequence

TATTTTTTATTGGATCGGAGCAAATCTTATATCTATGTAGAGGACATAAAAAAATGTGATAAGGATCAAAATAAGTTCAATGCGTTGGCGCACGGCTTAT[G/T,A]
TGTATGACGTACGTACCCTGGGTTGGGAGTGCGGGGAGTCGAGGCGGAACTCGTGCATAACCCAGCCGGTCTTGACGCCGTTGGGCGCCCTCCCCTGGTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.70%	16.20%	0.13%	0.00%	T: 0.04%
All Indica	2759	73.70%	26.20%	0.14%	0.00%	NA
All Japonica	1512	97.70%	2.20%	0.07%	0.00%	NA
Aus	269	98.90%	0.40%	0.00%	0.00%	T: 0.74%
Indica I	595	81.20%	18.70%	0.17%	0.00%	NA
Indica II	465	80.20%	19.80%	0.00%	0.00%	NA
Indica III	913	67.80%	32.20%	0.00%	0.00%	NA
Indica Intermediate	786	71.00%	28.60%	0.38%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	93.80%	6.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	7.80%	1.11%	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
vg0224817087	C -> A	LOC_Os02g40950.1	upstream_gene_variant ; 1752.0bp to feature; MODIFIER	silent_mutation	Average:67.994; most accessible tissue: Minghui63 root, score: 88.705	N	N	N	N
vg0224817087	C -> A	LOC_Os02g41450.1	intron_variant ; MODIFIER	silent_mutation	Average:67.994; most accessible tissue: Minghui63 root, score: 88.705	N	N	N	N
vg0224817087	C -> T	LOC_Os02g40950.1	upstream_gene_variant ; 1752.0bp to feature; MODIFIER	silent_mutation	Average:67.994; most accessible tissue: Minghui63 root, score: 88.705	N	N	N	N
vg0224817087	C -> T	LOC_Os02g41450.1	intron_variant ; MODIFIER	silent_mutation	Average:67.994; most accessible tissue: Minghui63 root, score: 88.705	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)
vg0224817087	C	A	-0.08	-0.08	-0.07	-0.08	-0.08	-0.07
vg0224817087	C	T	-0.05	-0.04	-0.03	-0.04	-0.04	-0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224817087	NA	3.69E-09	mr1078	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
vg0224817087	NA	1.09E-06	mr1211	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
vg0224817087	NA	2.92E-06	mr1561	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
vg0224817087	NA	7.75E-08	mr1068_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
vg0224817087	NA	1.63E-07	mr1078_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
vg0224817087	NA	1.83E-06	mr1099_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
vg0224817087	3.80E-06	NA	mr1124_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
vg0224817087	7.17E-06	NA	mr1124_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
vg0224817087	NA	2.60E-09	mr1200_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
vg0224817087	NA	1.13E-06	mr1211_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
vg0224817087	NA	8.39E-06	mr1561_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
vg0224817087	NA	3.47E-06	mr1913_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
vg0224817087	NA	1.53E-07	mr1929_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