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Detailed information for vg0205996999:

Variant ID: vg0205996999 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 5996999
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGCGGCTGGAAGGCGTCGGCGACGTCGGCGGCTAGGGCTACGCGGCGGCGGCGCTACGGACGATGGCTCGGCTTGGGACTTGAGGCAAACGGAAGAGGAC[G/A]
GCTAGGGGATGCTATTTATAGCCGGAAGAGGGAGAGATCGGCTCGGGAACGGATGGAATCGGCGACGGATTAGTTTGGGTTCGCCGGAAAATAGGAACTC

Reverse complement sequence

GAGTTCCTATTTTCCGGCGAACCCAAACTAATCCGTCGCCGATTCCATCCGTTCCCGAGCCGATCTCTCCCTCTTCCGGCTATAAATAGCATCCCCTAGC[C/T]
GTCCTCTTCCGTTTGCCTCAAGTCCCAAGCCGAGCCATCGTCCGTAGCGCCGCCGCCGCGTAGCCCTAGCCGCCGACGTCGCCGACGCCTTCCAGCCGCG

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	58.20%	1.60%	8.78%	31.42%	NA
All Indica	2759	38.10%	2.60%	13.48%	45.81%	NA
All Japonica	1512	97.80%	0.00%	0.46%	1.72%	NA
Aus	269	31.60%	0.40%	10.41%	57.62%	NA
Indica I	595	39.30%	1.50%	10.59%	48.57%	NA
Indica II	465	37.00%	0.90%	11.83%	50.32%	NA
Indica III	913	36.70%	3.30%	17.85%	42.17%	NA
Indica Intermediate	786	39.30%	3.80%	11.58%	45.29%	NA
Temperate Japonica	767	98.00%	0.00%	0.26%	1.69%	NA
Tropical Japonica	504	98.20%	0.00%	0.79%	0.99%	NA
Japonica Intermediate	241	96.30%	0.00%	0.41%	3.32%	NA
VI/Aromatic	96	81.20%	0.00%	4.17%	14.58%	NA
Intermediate	90	66.70%	0.00%	4.44%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0205996999	G -> A	LOC_Os02g11665.1	3_prime_UTR_variant ; 1079.0bp to feature; MODIFIER	silent_mutation	Average:79.791; most accessible tissue: Zhenshan97 flag leaf, score: 93.831	N	N	N	N
vg0205996999	G -> A	LOC_Os02g11660.1	upstream_gene_variant ; 3926.0bp to feature; MODIFIER	silent_mutation	Average:79.791; most accessible tissue: Zhenshan97 flag leaf, score: 93.831	N	N	N	N
vg0205996999	G -> DEL	N	N	silent_mutation	Average:79.791; most accessible tissue: Zhenshan97 flag leaf, score: 93.831	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)
vg0205996999	G	A	0.02	0.01	0.03	0.01	0.04	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0205996999	NA	1.48E-07	mr1238	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
vg0205996999	NA	5.35E-07	mr1309	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
vg0205996999	NA	1.94E-08	mr1841	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
vg0205996999	3.02E-07	3.02E-07	mr1900	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
vg0205996999	NA	4.00E-08	mr1238_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
vg0205996999	NA	1.72E-06	mr1484_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
vg0205996999	NA	4.33E-09	mr1841_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
vg0205996999	NA	2.10E-07	mr1900_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