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Detailed information for vg1125256580:

Variant ID: vg1125256580 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25256580
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATTTTCAAACTCAATAACTCGAGAGTTATTCATGATTTATATTTTCAAGGTTTGACTTAAACATTGTCATAAACGATTTTCTTTACGAGTACGGAGAGA[G/T]
GACATGATTTATGATTAAAGTCTGTTGAAATCAATCATTTGGAACATGCTATTATATGTTTTTTTTAACTTACTCAGACTTCTCTGTAATTTTTTTCTGG

Reverse complement sequence

CCAGAAAAAAATTACAGAGAAGTCTGAGTAAGTTAAAAAAAACATATAATAGCATGTTCCAAATGATTGATTTCAACAGACTTTAATCATAAATCATGTC[C/A]
TCTCTCCGTACTCGTAAAGAAAATCGTTTATGACAATGTTTAAGTCAAACCTTGAAAATATAAATCATGAATAACTCTCGAGTTATTGAGTTTGAAAATG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.60%	1.50%	1.31%	2.67%	NA
All Indica	2759	94.70%	0.90%	1.52%	2.90%	NA
All Japonica	1512	96.40%	1.10%	0.13%	2.38%	NA
Aus	269	84.80%	7.10%	6.32%	1.86%	NA
Indica I	595	98.80%	1.20%	0.00%	0.00%	NA
Indica II	465	85.60%	0.20%	5.38%	8.82%	NA
Indica III	913	98.60%	1.10%	0.00%	0.33%	NA
Indica Intermediate	786	92.40%	0.90%	2.16%	4.58%	NA
Temperate Japonica	767	98.60%	1.20%	0.00%	0.26%	NA
Tropical Japonica	504	95.40%	0.60%	0.40%	3.57%	NA
Japonica Intermediate	241	91.70%	1.70%	0.00%	6.64%	NA
VI/Aromatic	96	89.60%	8.30%	0.00%	2.08%	NA
Intermediate	90	94.40%	1.10%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125256580	G -> T	LOC_Os11g41990.1	upstream_gene_variant ; 3813.0bp to feature; MODIFIER	silent_mutation	Average:86.216; most accessible tissue: Minghui63 young leaf, score: 95.751	N	N	N	N
vg1125256580	G -> T	LOC_Os11g42000.1	upstream_gene_variant ; 1304.0bp to feature; MODIFIER	silent_mutation	Average:86.216; most accessible tissue: Minghui63 young leaf, score: 95.751	N	N	N	N
vg1125256580	G -> T	LOC_Os11g41990.2	upstream_gene_variant ; 3813.0bp to feature; MODIFIER	silent_mutation	Average:86.216; most accessible tissue: Minghui63 young leaf, score: 95.751	N	N	N	N
vg1125256580	G -> T	LOC_Os11g41990-LOC_Os11g42000	intergenic_region ; MODIFIER	silent_mutation	Average:86.216; most accessible tissue: Minghui63 young leaf, score: 95.751	N	N	N	N
vg1125256580	G -> DEL	N	N	silent_mutation	Average:86.216; most accessible tissue: Minghui63 young leaf, score: 95.751	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)
vg1125256580	G	T	-0.08	-0.07	-0.1	-0.03	-0.05	-0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125256580	2.50E-12	5.29E-14	mr1238	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
vg1125256580	2.64E-09	2.31E-10	mr1309	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
vg1125256580	NA	3.35E-06	mr1484	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
vg1125256580	1.64E-06	1.49E-07	mr1841	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
vg1125256580	5.27E-09	4.34E-11	mr1238_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
vg1125256580	1.46E-09	6.95E-12	mr1484_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
vg1125256580	1.24E-06	NA	mr1662_2	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
vg1125256580	1.80E-09	9.31E-12	mr1841_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
vg1125256580	3.19E-06	4.32E-08	mr1900_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
vg1125256580	7.72E-08	7.72E-08	mr1945_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