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Detailed information for vg0917042786:

Variant ID: vg0917042786 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 17042786
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCACTGCGCCCTTCACCGCACGGTAGTGCATCCTCCTCGTTCTCCCTCCTCGCTCCCTCTCCTCCCCTTAGCTTTAGGTAGTAGCACGAGTAGACCTCCC[G/A]
TAACTAGCTGGCGCCGCCCCGACCGCTGCCAATGCTCGCTGTGTGCTCGCCGCTGTCGCCGCCCGAGCTCGATAGCGCCTGCACGTCGCCGGCCTCTCTC

Reverse complement sequence

GAGAGAGGCCGGCGACGTGCAGGCGCTATCGAGCTCGGGCGGCGACAGCGGCGAGCACACAGCGAGCATTGGCAGCGGTCGGGGCGGCGCCAGCTAGTTA[C/T]
GGGAGGTCTACTCGTGCTACTACCTAAAGCTAAGGGGAGGAGAGGGAGCGAGGAGGGAGAACGAGGAGGATGCACTACCGTGCGGTGAAGGGCGCAGTGA

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	90.70%	0.60%	4.30%	4.36%	NA
All Indica	2759	99.80%	0.00%	0.07%	0.11%	NA
All Japonica	1512	74.90%	1.70%	11.38%	12.04%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.00%	0.13%	0.38%	NA
Temperate Japonica	767	95.00%	1.40%	2.48%	1.04%	NA
Tropical Japonica	504	35.30%	2.40%	28.77%	33.53%	NA
Japonica Intermediate	241	93.80%	0.80%	3.32%	2.07%	NA
VI/Aromatic	96	54.20%	4.20%	23.96%	17.71%	NA
Intermediate	90	88.90%	1.10%	5.56%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0917042786	G -> DEL	N	N	silent_mutation	Average:87.35; most accessible tissue: Minghui63 flag leaf, score: 96.628	N	N	N	N
vg0917042786	G -> A	LOC_Os09g28070.1	upstream_gene_variant ; 1960.0bp to feature; MODIFIER	silent_mutation	Average:87.35; most accessible tissue: Minghui63 flag leaf, score: 96.628	N	N	N	N
vg0917042786	G -> A	LOC_Os09g28060-LOC_Os09g28070	intergenic_region ; MODIFIER	silent_mutation	Average:87.35; most accessible tissue: Minghui63 flag leaf, score: 96.628	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)
vg0917042786	G	A	-0.02	-0.02	-0.02	-0.01	-0.02	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0917042786	3.61E-07	1.07E-13	mr1641	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
vg0917042786	NA	8.19E-06	mr1641	Jap_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
vg0917042786	NA	1.29E-11	mr1398_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
vg0917042786	NA	3.01E-07	mr1398_2	Jap_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
vg0917042786	NA	4.00E-07	mr1401_2	Jap_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
vg0917042786	NA	6.85E-08	mr1408_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
vg0917042786	NA	3.24E-09	mr1676_2	Jap_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
vg0917042786	NA	1.82E-08	mr1905_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
vg0917042786	NA	2.53E-10	mr1916_2	Jap_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