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Detailed information for vg1118460774:

Variant ID: vg1118460774 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 18460774
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

ATTCGTCTTATTAAAAAATATTAGAATTATTATTTATTTTATTTGTGACTTACTTTATTATCCAAAGTAACTTAATCATAACTTTTCTTTTTTATATTTA[C/T]
ATAAATTTTTTTGGATAAGACGAGTAGTCAAACAGTGTAATCAACATATTTTTATCGCTAGTATACCGTTACGGTTTACAATTAATTTTCGGGCGACGCA

Reverse complement sequence

TGCGTCGCCCGAAAATTAATTGTAAACCGTAACGGTATACTAGCGATAAAAATATGTTGATTACACTGTTTGACTACTCGTCTTATCCAAAAAAATTTAT[G/A]
TAAATATAAAAAAGAAAAGTTATGATTAAGTTACTTTGGATAATAAAGTAAGTCACAAATAAAATAAATAATAATTCTAATATTTTTTAATAAGACGAAT

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	51.50%	44.30%	3.81%	0.42%	NA
All Indica	2759	41.20%	57.00%	1.74%	0.04%	NA
All Japonica	1512	70.30%	20.00%	8.47%	1.19%	NA
Aus	269	31.20%	68.00%	0.37%	0.37%	NA
Indica I	595	28.40%	69.10%	2.52%	0.00%	NA
Indica II	465	61.50%	38.30%	0.22%	0.00%	NA
Indica III	913	38.40%	60.20%	1.20%	0.11%	NA
Indica Intermediate	786	42.10%	55.20%	2.67%	0.00%	NA
Temperate Japonica	767	49.40%	32.90%	15.38%	2.35%	NA
Tropical Japonica	504	96.40%	3.00%	0.60%	0.00%	NA
Japonica Intermediate	241	82.20%	14.90%	2.90%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	63.30%	33.30%	3.33%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1118460774	C -> T	LOC_Os11g31590.1	downstream_gene_variant ; 3446.0bp to feature; MODIFIER	silent_mutation	Average:77.396; most accessible tissue: Minghui63 panicle, score: 95.915	N	N	N	N
vg1118460774	C -> T	LOC_Os11g31570-LOC_Os11g31590	intergenic_region ; MODIFIER	silent_mutation	Average:77.396; most accessible tissue: Minghui63 panicle, score: 95.915	N	N	N	N
vg1118460774	C -> DEL	N	N	silent_mutation	Average:77.396; most accessible tissue: Minghui63 panicle, score: 95.915	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)
vg1118460774	C	T	0.03	0.02	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
vg1118460774	NA	9.32E-06	mr1006	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
vg1118460774	NA	1.55E-07	mr1010	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
vg1118460774	1.26E-06	2.79E-08	mr1013	Jap_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
vg1118460774	2.03E-06	5.19E-08	mr1031	Jap_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
vg1118460774	1.56E-06	6.42E-08	mr1034	Jap_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
vg1118460774	9.99E-06	2.79E-07	mr1056	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
vg1118460774	NA	9.63E-08	mr1163	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
vg1118460774	NA	5.42E-06	mr1502	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
vg1118460774	NA	6.87E-06	mr1627	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
vg1118460774	NA	2.46E-07	mr1956	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
vg1118460774	NA	1.45E-07	mr1517_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
vg1118460774	NA	1.02E-06	mr1554_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
vg1118460774	NA	3.47E-07	mr1915_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
vg1118460774	NA	2.83E-07	mr1925_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