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Detailed information for vg1121671958:

Variant ID: vg1121671958 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21671958
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTTTGCGTGGAGGAGAGGGGCGGCGGGGGCGGCAAGAAGTGGCCGGGCTTCGTCCAGTTCTTCTTCGTCCTCTCCGTGGTCCTCTGCGTGCTCCTCTAC[G/A]
CCCCGCGGTTCATCGTGCTTACGCCCACCTACGGCCTCGACTTCTTCCCCAGCCGCCGCCCAACGACACCACCTCGACCGCCCGCGTCGTGGGAGATCAT

Reverse complement sequence

ATGATCTCCCACGACGCGGGCGGTCGAGGTGGTGTCGTTGGGCGGCGGCTGGGGAAGAAGTCGAGGCCGTAGGTGGGCGTAAGCACGATGAACCGCGGGG[C/T]
GTAGAGGAGCACGCAGAGGACCACGGAGAGGACGAAGAAGAACTGGACGAAGCCCGGCCACTTCTTGCCGCCCCCGCCGCCCCTCTCCTCCACGCAAAGT

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	59.00%	5.80%	1.29%	33.90%	NA
All Indica	2759	49.00%	6.40%	1.85%	42.77%	NA
All Japonica	1512	80.20%	2.10%	0.40%	17.33%	NA
Aus	269	56.50%	23.00%	0.37%	20.07%	NA
Indica I	595	43.20%	26.60%	1.85%	28.40%	NA
Indica II	465	45.20%	0.00%	2.37%	52.47%	NA
Indica III	913	51.40%	0.50%	1.42%	46.66%	NA
Indica Intermediate	786	52.80%	1.80%	2.04%	43.38%	NA
Temperate Japonica	767	89.20%	1.60%	0.13%	9.13%	NA
Tropical Japonica	504	71.40%	1.80%	0.79%	25.99%	NA
Japonica Intermediate	241	69.70%	4.60%	0.41%	25.31%	NA
VI/Aromatic	96	12.50%	0.00%	2.08%	85.42%	NA
Intermediate	90	70.00%	2.20%	1.11%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121671958	G -> A	LOC_Os11g36700.1	upstream_gene_variant ; 406.0bp to feature; MODIFIER	silent_mutation	Average:41.373; most accessible tissue: Minghui63 flower, score: 83.722	N	N	N	N
vg1121671958	G -> A	LOC_Os11g36719.1	upstream_gene_variant ; 3069.0bp to feature; MODIFIER	silent_mutation	Average:41.373; most accessible tissue: Minghui63 flower, score: 83.722	N	N	N	N
vg1121671958	G -> A	LOC_Os11g36690.1	downstream_gene_variant ; 4792.0bp to feature; MODIFIER	silent_mutation	Average:41.373; most accessible tissue: Minghui63 flower, score: 83.722	N	N	N	N
vg1121671958	G -> A	LOC_Os11g36690-LOC_Os11g36700	intergenic_region ; MODIFIER	silent_mutation	Average:41.373; most accessible tissue: Minghui63 flower, score: 83.722	N	N	N	N
vg1121671958	G -> DEL	N	N	silent_mutation	Average:41.373; most accessible tissue: Minghui63 flower, score: 83.722	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)
vg1121671958	G	A	0.0	0.0	0.0	0.0	-0.01	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121671958	NA	8.16E-08	mr1291_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
vg1121671958	NA	4.43E-06	mr1479_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
vg1121671958	3.47E-06	4.17E-08	mr1502_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
vg1121671958	NA	8.97E-06	mr1543_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
vg1121671958	NA	5.30E-06	mr1662_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
vg1121671958	NA	4.54E-08	mr1709_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
vg1121671958	NA	2.26E-07	mr1742_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