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Detailed information for vg0500775033:

Variant ID: vg0500775033 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 775033
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTGCTGACGTGGCGCCTATGTGGTGGTAATTATCGGGTCTCCTTTACACGTGATGTTGAGGTGGCATTTAGAATTTAAAAATATATGTGGGATCCATTT[G/A]
TCAGCGACACATAAAAAAAATTGTGGGACACGTCTCTCCCCTCCCTCTCCCTCCAGTTCCTTCTCTCTCCTCGCCAGTCGCCACTCCCTCTCTCTCTCTC

Reverse complement sequence

GAGAGAGAGAGAGGGAGTGGCGACTGGCGAGGAGAGAGAAGGAACTGGAGGGAGAGGGAGGGGAGAGACGTGTCCCACAATTTTTTTTATGTGTCGCTGA[C/T]
AAATGGATCCCACATATATTTTTAAATTCTAAATGCCACCTCAACATCACGTGTAAAGGAGACCCGATAATTACCACCACATAGGCGCCACGTCAGCAAA

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	78.70%	4.40%	7.77%	9.18%	NA
All Indica	2759	75.20%	0.90%	8.74%	15.19%	NA
All Japonica	1512	91.90%	0.50%	7.28%	0.33%	NA
Aus	269	38.70%	60.60%	0.00%	0.74%	NA
Indica I	595	81.50%	0.00%	2.69%	15.80%	NA
Indica II	465	81.90%	0.00%	6.02%	12.04%	NA
Indica III	913	63.00%	0.40%	16.43%	20.15%	NA
Indica Intermediate	786	80.50%	2.70%	5.98%	10.81%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	79.20%	0.00%	20.44%	0.40%	NA
Japonica Intermediate	241	93.40%	2.50%	2.90%	1.24%	NA
VI/Aromatic	96	76.00%	9.40%	11.46%	3.12%	NA
Intermediate	90	86.70%	2.20%	5.56%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0500775033	G -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500775033	G -> A	LOC_Os05g02360.1	upstream_gene_variant ; 3573.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500775033	G -> A	LOC_Os05g02370.1	upstream_gene_variant ; 1409.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500775033	G -> A	LOC_Os05g02370-LOC_Os05g02390	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	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)
vg0500775033	G	A	-0.04	-0.05	-0.03	-0.05	-0.03	-0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0500775033	NA	1.26E-06	mr1184	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
vg0500775033	NA	3.37E-08	mr1262	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
vg0500775033	NA	8.49E-06	mr1289	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
vg0500775033	NA	3.70E-08	mr1365	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
vg0500775033	NA	4.89E-42	mr1550	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
vg0500775033	NA	4.81E-07	mr1556	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
vg0500775033	NA	2.37E-06	mr1574	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
vg0500775033	NA	5.36E-06	mr1621	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
vg0500775033	4.27E-07	NA	mr1705	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
vg0500775033	NA	1.62E-06	mr1735	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
vg0500775033	NA	2.82E-06	mr1774	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
vg0500775033	NA	8.84E-12	mr1897	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