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Detailed information for vg1118170898:

Variant ID: vg1118170898 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 18170898
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGCCTGCAAGAGCCAGGAATGTTGGGCCGCGGTTGTGCCGATTGTTGGACCATGCCGTGCTGGGCTGGCATGTCGTGTCAAGTAAGAGACCCAGAAACG[G/A]
CCCGACGGTCGGGTCGGGTCGGGCCAGCACAGGCCTAACAACAGTCGAGCCGTGTCGTGTCTGGGCTGGGCCAAATCTTCATACCATGGGTCGGGCCGTC

Reverse complement sequence

GACGGCCCGACCCATGGTATGAAGATTTGGCCCAGCCCAGACACGACACGGCTCGACTGTTGTTAGGCCTGTGCTGGCCCGACCCGACCCGACCGTCGGG[C/T]
CGTTTCTGGGTCTCTTACTTGACACGACATGCCAGCCCAGCACGGCATGGTCCAACAATCGGCACAACCGCGGCCCAACATTCCTGGCTCTTGCAGGCCG

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	87.20%	11.90%	0.89%	0.00%	NA
All Indica	2759	87.50%	11.70%	0.76%	0.00%	NA
All Japonica	1512	98.10%	0.70%	1.19%	0.00%	NA
Aus	269	31.60%	67.30%	1.12%	0.00%	NA
Indica I	595	98.00%	1.80%	0.17%	0.00%	NA
Indica II	465	96.60%	1.50%	1.94%	0.00%	NA
Indica III	913	77.30%	22.30%	0.33%	0.00%	NA
Indica Intermediate	786	86.00%	13.00%	1.02%	0.00%	NA
Temperate Japonica	767	97.90%	0.00%	2.09%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	96.30%	3.30%	0.41%	0.00%	NA
VI/Aromatic	96	57.30%	42.70%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	0.00%	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
vg1118170898	G -> A	LOC_Os11g31190.1	downstream_gene_variant ; 780.0bp to feature; MODIFIER	silent_mutation	Average:97.836; most accessible tissue: Minghui63 root, score: 99.988	N	N	N	N
vg1118170898	G -> A	LOC_Os11g31180-LOC_Os11g31190	intergenic_region ; MODIFIER	silent_mutation	Average:97.836; most accessible tissue: Minghui63 root, score: 99.988	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)
vg1118170898	G	A	-0.04	-0.04	-0.04	-0.02	-0.03	-0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1118170898	NA	2.57E-07	mr1028	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
vg1118170898	NA	2.03E-06	mr1126	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
vg1118170898	NA	3.59E-06	mr1262	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
vg1118170898	NA	5.29E-06	mr1397	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
vg1118170898	NA	6.01E-08	mr1453	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
vg1118170898	NA	9.55E-07	mr1574	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
vg1118170898	NA	2.87E-08	mr1652	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
vg1118170898	NA	1.27E-10	mr1866	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
vg1118170898	4.65E-07	4.65E-07	mr1866	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