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Detailed information for vg0102177568:

Variant ID: vg0102177568 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 2177568
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCAGCATCATCCATCTGCTCCCCAGCCCCAACACGACAAATAAAAGCCGGAGAGAGAGAGAGCAGGTATAATAGATAAACAGTTATAAATATATTTTAAA[G/A]
AGATAAAAGAAAAGAGAGAAAAGTAACGGGCTATAAATTTGTAGCCAGCTACAGCATGGCCTTCAAGATATAATGTATGTATGATAGATAGGACCATATA

Reverse complement sequence

TATATGGTCCTATCTATCATACATACATTATATCTTGAAGGCCATGCTGTAGCTGGCTACAAATTTATAGCCCGTTACTTTTCTCTCTTTTCTTTTATCT[C/T]
TTTAAAATATATTTATAACTGTTTATCTATTATACCTGCTCTCTCTCTCTCCGGCTTTTATTTGTCGTGTTGGGGCTGGGGAGCAGATGGATGATGCTGG

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	78.50%	1.60%	2.14%	17.84%	NA
All Indica	2759	90.30%	2.30%	1.27%	6.16%	NA
All Japonica	1512	63.50%	0.10%	3.44%	32.94%	NA
Aus	269	35.30%	1.10%	4.09%	59.48%	NA
Indica I	595	99.70%	0.00%	0.00%	0.34%	NA
Indica II	465	99.10%	0.00%	0.00%	0.86%	NA
Indica III	913	82.30%	3.30%	3.18%	11.28%	NA
Indica Intermediate	786	87.20%	4.30%	0.76%	7.76%	NA
Temperate Japonica	767	95.20%	0.10%	0.13%	4.56%	NA
Tropical Japonica	504	21.20%	0.20%	9.72%	68.85%	NA
Japonica Intermediate	241	51.00%	0.00%	0.83%	48.13%	NA
VI/Aromatic	96	95.80%	1.00%	0.00%	3.12%	NA
Intermediate	90	78.90%	4.40%	3.33%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0102177568	G -> A	LOC_Os01g04770.1	upstream_gene_variant ; 3778.0bp to feature; MODIFIER	silent_mutation	Average:97.226; most accessible tissue: Zhenshan97 young leaf, score: 99.542	N	N	N	N
vg0102177568	G -> A	LOC_Os01g04760-LOC_Os01g04770	intergenic_region ; MODIFIER	silent_mutation	Average:97.226; most accessible tissue: Zhenshan97 young leaf, score: 99.542	N	N	N	N
vg0102177568	G -> DEL	N	N	silent_mutation	Average:97.226; most accessible tissue: Zhenshan97 young leaf, score: 99.542	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)
vg0102177568	G	A	0.02	0.01	0.02	0.02	0.01	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0102177568	7.85E-07	NA	mr1728	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
vg0102177568	NA	2.00E-08	mr1916	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
vg0102177568	NA	5.96E-07	mr1042_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
vg0102177568	NA	4.13E-07	mr1244_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
vg0102177568	NA	1.55E-11	mr1354_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
vg0102177568	NA	2.84E-06	mr1363_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
vg0102177568	NA	1.26E-07	mr1582_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
vg0102177568	NA	1.02E-14	mr1769_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
vg0102177568	NA	2.66E-09	mr1871_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