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Detailed information for vg0109768649:

Variant ID: vg0109768649 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 9768649
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAAGAGGCTCAAACCATGGGTGACTGAAATATGTTGCGGACTTCATAAGTTTTCAAGTCTTTTACTTTTATCTTGTCTTAGTGCCTGTTTAGTTCCCAA[A/G]
CAAAATTTTTCACGTTGTCACATCGAATGTTTGGACATATGCATGGAGTATTAAATGTAGACAAAAAAAAATCAATTACACAGTTCGCTAGGAAATTGCC

Reverse complement sequence

GGCAATTTCCTAGCGAACTGTGTAATTGATTTTTTTTTGTCTACATTTAATACTCCATGCATATGTCCAAACATTCGATGTGACAACGTGAAAAATTTTG[T/C]
TTGGGAACTAAACAGGCACTAAGACAAGATAAAAGTAAAAGACTTGAAAACTTATGAAGTCCGCAACATATTTCAGTCACCCATGGTTTGAGCCTCTTTG

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	57.70%	42.20%	0.08%	0.04%	NA
All Indica	2759	90.80%	9.00%	0.11%	0.07%	NA
All Japonica	1512	3.30%	96.60%	0.07%	0.00%	NA
Aus	269	13.00%	87.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.30%	0.00%	0.17%	NA
Indica II	465	85.20%	14.80%	0.00%	0.00%	NA
Indica III	913	89.70%	10.10%	0.22%	0.00%	NA
Indica Intermediate	786	88.80%	10.90%	0.13%	0.13%	NA
Temperate Japonica	767	1.70%	98.20%	0.13%	0.00%	NA
Tropical Japonica	504	5.40%	94.60%	0.00%	0.00%	NA
Japonica Intermediate	241	4.10%	95.90%	0.00%	0.00%	NA
VI/Aromatic	96	89.60%	10.40%	0.00%	0.00%	NA
Intermediate	90	55.60%	44.40%	0.00%	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
vg0109768649	A -> G	LOC_Os01g17040.1	downstream_gene_variant ; 2168.0bp to feature; MODIFIER	silent_mutation	Average:73.021; most accessible tissue: Zhenshan97 flag leaf, score: 88.993	N	N	N	N
vg0109768649	A -> G	LOC_Os01g17050.1	downstream_gene_variant ; 1366.0bp to feature; MODIFIER	silent_mutation	Average:73.021; most accessible tissue: Zhenshan97 flag leaf, score: 88.993	N	N	N	N
vg0109768649	A -> G	LOC_Os01g17040-LOC_Os01g17050	intergenic_region ; MODIFIER	silent_mutation	Average:73.021; most accessible tissue: Zhenshan97 flag leaf, score: 88.993	N	N	N	N
vg0109768649	A -> DEL	N	N	silent_mutation	Average:73.021; most accessible tissue: Zhenshan97 flag leaf, score: 88.993	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)
vg0109768649	A	G	0.01	0.02	0.01	0.01	0.01	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0109768649	NA	1.55E-17	mr1913	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
vg0109768649	NA	3.23E-15	mr1916	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
vg0109768649	NA	4.38E-12	mr1151_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
vg0109768649	NA	3.81E-10	mr1228_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
vg0109768649	1.13E-06	4.05E-09	mr1310_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
vg0109768649	NA	2.81E-11	mr1728_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
vg0109768649	NA	2.07E-45	mr1793_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
vg0109768649	NA	3.93E-26	mr1943_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