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Detailed information for vg1018182214:

Variant ID: vg1018182214 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 18182214
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.61, C: 0.38, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

AATCCTAGTATTATATTGCCATTTTCTTAAAAGAATCCTTAATTTTTTGTATTTCTAATATATATATAAATATATAAATGTATTCCCGTATCCTTGTTTT[T/C]
TGGAAAATACCGTATCCATGTATCGACGTATCGAGGTAGCATAGGTTACCATGGGAGATCGAGCCAAGGAGTAAAAAAAAAAGTAAAAGTAACAGCGACG

Reverse complement sequence

CGTCGCTGTTACTTTTACTTTTTTTTTTACTCCTTGGCTCGATCTCCCATGGTAACCTATGCTACCTCGATACGTCGATACATGGATACGGTATTTTCCA[A/G]
AAAACAAGGATACGGGAATACATTTATATATTTATATATATATTAGAAATACAAAAAATTAAGGATTCTTTTAAGAAAATGGCAATATAATACTAGGATT

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	65.20%	32.50%	1.59%	0.76%	NA
All Indica	2759	93.60%	3.70%	2.57%	0.14%	NA
All Japonica	1512	14.00%	85.80%	0.20%	0.00%	NA
Aus	269	86.20%	1.90%	0.00%	11.90%	NA
Indica I	595	90.30%	3.20%	6.55%	0.00%	NA
Indica II	465	93.50%	4.70%	1.51%	0.22%	NA
Indica III	913	96.30%	2.70%	0.99%	0.00%	NA
Indica Intermediate	786	93.10%	4.50%	2.04%	0.38%	NA
Temperate Japonica	767	1.40%	98.60%	0.00%	0.00%	NA
Tropical Japonica	504	38.10%	61.30%	0.60%	0.00%	NA
Japonica Intermediate	241	3.30%	96.70%	0.00%	0.00%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	51.10%	47.80%	1.11%	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
vg1018182214	T -> C	LOC_Os10g34064.1	upstream_gene_variant ; 2937.0bp to feature; MODIFIER	silent_mutation	Average:81.915; most accessible tissue: Callus, score: 99.066	N	N	N	N
vg1018182214	T -> C	LOC_Os10g34071.1	upstream_gene_variant ; 4935.0bp to feature; MODIFIER	silent_mutation	Average:81.915; most accessible tissue: Callus, score: 99.066	N	N	N	N
vg1018182214	T -> C	LOC_Os10g34050-LOC_Os10g34064	intergenic_region ; MODIFIER	silent_mutation	Average:81.915; most accessible tissue: Callus, score: 99.066	N	N	N	N
vg1018182214	T -> DEL	N	N	silent_mutation	Average:81.915; most accessible tissue: Callus, score: 99.066	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)
vg1018182214	T	C	-0.02	-0.01	-0.01	-0.01	-0.01	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1018182214	NA	4.00E-06	mr1076	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
vg1018182214	NA	7.69E-06	mr1083	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
vg1018182214	8.18E-06	NA	mr1103	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
vg1018182214	7.86E-07	NA	mr1104	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
vg1018182214	4.96E-07	NA	mr1226	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
vg1018182214	NA	1.96E-06	mr1226	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
vg1018182214	NA	9.53E-39	mr1645	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
vg1018182214	4.25E-06	NA	mr1082_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
vg1018182214	NA	1.02E-06	mr1082_2	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
vg1018182214	1.87E-06	NA	mr1226_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
vg1018182214	NA	5.98E-06	mr1226_2	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
vg1018182214	NA	1.39E-18	mr1336_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
vg1018182214	NA	1.34E-38	mr1689_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
vg1018182214	NA	3.61E-14	mr1790_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