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Detailed information for vg1122003053:

Variant ID: vg1122003053 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22003053
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATGGAAGCGGAGCTGAGTGGAGCACTCGCATAAAATAAACTAGAGAGATGTGAAGGTGGATTTAGACAACTCCACAACTTCACTACAGACCTAATTTCT[G/A]
AAGCTAAAGTTAGAAGTTAGAGCTCTATTAAACAGACCCTAAAACACAGTTGGACTAAGAAACGCTTGAAGAAAGGAAAAAAACTGCAATATCTTATTTC

Reverse complement sequence

GAAATAAGATATTGCAGTTTTTTTCCTTTCTTCAAGCGTTTCTTAGTCCAACTGTGTTTTAGGGTCTGTTTAATAGAGCTCTAACTTCTAACTTTAGCTT[C/T]
AGAAATTAGGTCTGTAGTGAAGTTGTGGAGTTGTCTAAATCCACCTTCACATCTCTCTAGTTTATTTTATGCGAGTGCTCCACTCAGCTCCGCTTCCATT

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	85.90%	9.00%	0.30%	4.85%	NA
All Indica	2759	91.10%	4.80%	0.22%	3.84%	NA
All Japonica	1512	79.60%	17.90%	0.20%	2.38%	NA
Aus	269	73.60%	1.10%	1.49%	23.79%	NA
Indica I	595	94.50%	5.00%	0.17%	0.34%	NA
Indica II	465	98.70%	0.90%	0.00%	0.43%	NA
Indica III	913	85.80%	6.70%	0.22%	7.34%	NA
Indica Intermediate	786	90.30%	4.80%	0.38%	4.45%	NA
Temperate Japonica	767	96.00%	3.10%	0.26%	0.65%	NA
Tropical Japonica	504	62.10%	32.70%	0.20%	4.96%	NA
Japonica Intermediate	241	63.90%	33.60%	0.00%	2.49%	NA
VI/Aromatic	96	76.00%	5.20%	1.04%	17.71%	NA
Intermediate	90	77.80%	15.60%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122003053	G -> A	LOC_Os11g37260.1	upstream_gene_variant ; 315.0bp to feature; MODIFIER	silent_mutation	Average:86.049; most accessible tissue: Callus, score: 92.754	N	N	N	N
vg1122003053	G -> A	LOC_Os11g37240.1	downstream_gene_variant ; 4535.0bp to feature; MODIFIER	silent_mutation	Average:86.049; most accessible tissue: Callus, score: 92.754	N	N	N	N
vg1122003053	G -> A	LOC_Os11g37250.1	downstream_gene_variant ; 1484.0bp to feature; MODIFIER	silent_mutation	Average:86.049; most accessible tissue: Callus, score: 92.754	N	N	N	N
vg1122003053	G -> A	LOC_Os11g37250-LOC_Os11g37260	intergenic_region ; MODIFIER	silent_mutation	Average:86.049; most accessible tissue: Callus, score: 92.754	N	N	N	N
vg1122003053	G -> DEL	N	N	silent_mutation	Average:86.049; most accessible tissue: Callus, score: 92.754	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)
vg1122003053	G	A	0.0	-0.01	-0.02	0.01	-0.01	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122003053	3.39E-06	NA	mr1698	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
vg1122003053	NA	4.28E-06	mr1698	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
vg1122003053	NA	7.46E-06	mr1428_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