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Detailed information for vg0519769031:

Variant ID: vg0519769031 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 19769031
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: 97. )

Flanking Sequence (100 bp) in Reference Genome:

CGCGGCGGCGGCGGCGGGGGATCGGAGGGGGAGCAGGGCCACTCGGATGGTATTGGGCTTCGCCGGCGCCGGAGGCGGCGATCGCGGATGGGCGGCGGGC[G/A]
GGGCGGGGGCCGGGGGTTGTAGGTGGAGGAGGAGGAGGGGCGGTTCCGGAGTTTGGGGAGGGGGCGGCGGTGCTCGTGCTGGGGGAGGAGTGGGGAGGAG

Reverse complement sequence

CTCCTCCCCACTCCTCCCCCAGCACGAGCACCGCCGCCCCCTCCCCAAACTCCGGAACCGCCCCTCCTCCTCCTCCACCTACAACCCCCGGCCCCCGCCC[C/T]
GCCCGCCGCCCATCCGCGATCGCCGCCTCCGGCGCCGGCGAAGCCCAATACCATCCGAGTGGCCCTGCTCCCCCTCCGATCCCCCGCCGCCGCCGCCGCG

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	72.80%	20.40%	5.06%	1.71%	NA
All Indica	2759	60.20%	33.40%	4.68%	1.67%	NA
All Japonica	1512	89.90%	0.80%	7.08%	2.25%	NA
Aus	269	92.60%	7.40%	0.00%	0.00%	NA
Indica I	595	34.50%	55.60%	9.24%	0.67%	NA
Indica II	465	59.40%	38.90%	1.29%	0.43%	NA
Indica III	913	69.80%	24.30%	2.85%	3.07%	NA
Indica Intermediate	786	69.20%	23.90%	5.34%	1.53%	NA
Temperate Japonica	767	82.40%	0.80%	12.78%	4.04%	NA
Tropical Japonica	504	98.80%	0.80%	0.00%	0.40%	NA
Japonica Intermediate	241	95.00%	0.80%	3.73%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	12.20%	3.33%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0519769031	G -> DEL	N	N	silent_mutation	Average:98.12; most accessible tissue: Zhenshan97 flag leaf, score: 98.947	N	N	N	N
vg0519769031	G -> A	LOC_Os05g33610.1	5_prime_UTR_variant ; 112.0bp to feature; MODIFIER	silent_mutation	Average:98.12; most accessible tissue: Zhenshan97 flag leaf, score: 98.947	N	N	N	N
vg0519769031	G -> A	LOC_Os05g33610.3	5_prime_UTR_variant ; 112.0bp to feature; MODIFIER	silent_mutation	Average:98.12; most accessible tissue: Zhenshan97 flag leaf, score: 98.947	N	N	N	N
vg0519769031	G -> A	LOC_Os05g33610.2	5_prime_UTR_variant ; 112.0bp to feature; MODIFIER	silent_mutation	Average:98.12; most accessible tissue: Zhenshan97 flag leaf, score: 98.947	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)
vg0519769031	G	A	-0.01	-0.01	0.0	0.0	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0519769031	NA	2.55E-10	mr1322_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
vg0519769031	NA	6.97E-07	mr1322_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
vg0519769031	NA	3.69E-06	mr1324_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
vg0519769031	NA	2.06E-12	mr1325_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
vg0519769031	NA	2.82E-06	mr1325_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
vg0519769031	NA	1.57E-13	mr1326_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
vg0519769031	NA	5.55E-07	mr1326_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
vg0519769031	NA	5.16E-06	mr1333_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
vg0519769031	NA	4.19E-07	mr1623_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
vg0519769031	1.77E-06	9.30E-06	mr1719_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
vg0519769031	2.51E-06	1.42E-06	mr1719_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
vg0519769031	NA	5.88E-06	mr1785_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
vg0519769031	NA	1.23E-06	mr1925_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