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Detailed information for vg1006976423:

Variant ID: vg1006976423 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 6976423
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAAGCAATGTCCTCCCTAACTACGGCCCAAGCCCAACAACTGATCAGTGGTCGGTTCATCATCCTCGTAGGGCACACCCACGACACGGCCGCCGCCGCC[G/A]
TAGTATCAGGGAGGGATTAAGTGAAAACGTGAGAGGCGGCCGCACCGTCGTCTCCACGCTGACTACGGCACTACGCCAATAGGCTGCGGTCTGCGGACAC

Reverse complement sequence

GTGTCCGCAGACCGCAGCCTATTGGCGTAGTGCCGTAGTCAGCGTGGAGACGACGGTGCGGCCGCCTCTCACGTTTTCACTTAATCCCTCCCTGATACTA[C/T]
GGCGGCGGCGGCCGTGTCGTGGGTGTGCCCTACGAGGATGATGAACCGACCACTGATCAGTTGTTGGGCTTGGGCCGTAGTTAGGGAGGACATTGCTTTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.20%	24.30%	0.19%	0.32%	NA
All Indica	2759	98.00%	1.90%	0.04%	0.04%	NA
All Japonica	1512	31.40%	68.50%	0.00%	0.07%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	99.00%	1.00%	0.00%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	97.30%	2.50%	0.11%	0.11%	NA
Indica Intermediate	786	98.20%	1.80%	0.00%	0.00%	NA
Temperate Japonica	767	16.20%	83.80%	0.00%	0.00%	NA
Tropical Japonica	504	50.00%	50.00%	0.00%	0.00%	NA
Japonica Intermediate	241	41.10%	58.50%	0.00%	0.41%	NA
VI/Aromatic	96	55.20%	27.10%	7.29%	10.42%	NA
Intermediate	90	61.10%	34.40%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1006976423	G -> A	LOC_Os10g12530.1	upstream_gene_variant ; 4322.0bp to feature; MODIFIER	silent_mutation	Average:74.22; most accessible tissue: Zhenshan97 young leaf, score: 88.878	N	N	N	N
vg1006976423	G -> A	LOC_Os10g12539.1	downstream_gene_variant ; 1900.0bp to feature; MODIFIER	silent_mutation	Average:74.22; most accessible tissue: Zhenshan97 young leaf, score: 88.878	N	N	N	N
vg1006976423	G -> A	LOC_Os10g12548.1	downstream_gene_variant ; 3062.0bp to feature; MODIFIER	silent_mutation	Average:74.22; most accessible tissue: Zhenshan97 young leaf, score: 88.878	N	N	N	N
vg1006976423	G -> A	LOC_Os10g12530-LOC_Os10g12539	intergenic_region ; MODIFIER	silent_mutation	Average:74.22; most accessible tissue: Zhenshan97 young leaf, score: 88.878	N	N	N	N
vg1006976423	G -> DEL	N	N	silent_mutation	Average:74.22; most accessible tissue: Zhenshan97 young leaf, score: 88.878	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)
vg1006976423	G	A	-0.43	-0.19	-0.12	-0.25	-0.26	-0.24

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1006976423	NA	8.48E-10	mr1622	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
vg1006976423	NA	5.27E-09	mr1806	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
vg1006976423	NA	2.60E-12	mr1986	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
vg1006976423	NA	6.10E-12	mr1986_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