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Detailed information for vg1109260557:

Variant ID: vg1109260557 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9260557
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

CCCAAGAAATCCCCAAAAGTTTCTACGGAAATCCTTTCCAATTTCGCGGTTCAATTTTTCCTTTTTCCGGCGAGAACCCTAGATTTTCCCGAGTTTTTCC[C/T]
GTCGATGTGGGCTTGATCCCGAGCTCCCGTGCCTATATAAAGGACCCCCTCGTCGTACTCTACCTATCCCCTCAAGTCCCGTCCTCCACCGTCGCCGCAA

Reverse complement sequence

TTGCGGCGACGGTGGAGGACGGGACTTGAGGGGATAGGTAGAGTACGACGAGGGGGTCCTTTATATAGGCACGGGAGCTCGGGATCAAGCCCACATCGAC[G/A]
GGAAAAACTCGGGAAAATCTAGGGTTCTCGCCGGAAAAAGGAAAAATTGAACCGCGAAATTGGAAAGGATTTCCGTAGAAACTTTTGGGGATTTCTTGGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.80%	14.10%	0.63%	35.44%	NA
All Indica	2759	17.00%	23.30%	1.01%	58.68%	NA
All Japonica	1512	97.60%	0.10%	0.07%	2.25%	NA
Aus	269	98.10%	1.10%	0.37%	0.37%	NA
Indica I	595	23.00%	0.80%	1.01%	75.13%	NA
Indica II	465	6.20%	56.30%	0.65%	36.77%	NA
Indica III	913	12.90%	24.10%	0.99%	61.99%	NA
Indica Intermediate	786	23.40%	20.00%	1.27%	55.34%	NA
Temperate Japonica	767	97.40%	0.00%	0.00%	2.61%	NA
Tropical Japonica	504	97.20%	0.40%	0.20%	2.18%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	58.90%	18.90%	0.00%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109260557	C -> T	LOC_Os11g16690.1	upstream_gene_variant ; 3499.0bp to feature; MODIFIER	silent_mutation	Average:56.204; most accessible tissue: Minghui63 flag leaf, score: 90.512	N	N	N	N
vg1109260557	C -> T	LOC_Os11g16720.1	upstream_gene_variant ; 3780.0bp to feature; MODIFIER	silent_mutation	Average:56.204; most accessible tissue: Minghui63 flag leaf, score: 90.512	N	N	N	N
vg1109260557	C -> T	LOC_Os11g16710.1	downstream_gene_variant ; 64.0bp to feature; MODIFIER	silent_mutation	Average:56.204; most accessible tissue: Minghui63 flag leaf, score: 90.512	N	N	N	N
vg1109260557	C -> T	LOC_Os11g16690-LOC_Os11g16710	intergenic_region ; MODIFIER	silent_mutation	Average:56.204; most accessible tissue: Minghui63 flag leaf, score: 90.512	N	N	N	N
vg1109260557	C -> DEL	N	N	silent_mutation	Average:56.204; most accessible tissue: Minghui63 flag leaf, score: 90.512	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)
vg1109260557	C	T	-0.01	-0.01	-0.03	-0.01	-0.02	-0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109260557	NA	4.76E-06	mr1352	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
vg1109260557	NA	2.63E-07	mr1609	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
vg1109260557	NA	6.80E-06	mr1805	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
vg1109260557	NA	8.66E-06	mr1806	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
vg1109260557	NA	1.48E-07	mr1829	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
vg1109260557	NA	1.25E-10	mr1829	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
vg1109260557	NA	7.40E-07	mr1842	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
vg1109260557	NA	1.77E-09	mr1902	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
vg1109260557	NA	2.38E-10	mr1829_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
vg1109260557	NA	1.29E-06	mr1842_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
vg1109260557	NA	3.78E-09	mr1902_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
vg1109260557	NA	8.16E-07	mr1933_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