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Detailed information for vg0701246321:

Variant ID: vg0701246321 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 1246321
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, C: 0.08, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

TGGGGGAGAGAGAGAGAGAGGAGGGAAGAGGAAGACTTTGGGGAAAGCGAAGTTTGACGAGGAGATGAGCTGAGACGAGGGGCGGTGGTGCAAGTGGTGT[T/C]
GCTGCGTGGCGAATCGATGTGGTTGAGCTGCCTGTCAGTCACTGAGAGCAGGGATAATAATAGGACTCACTTCTTACTATTAATTAATCTTAAAGCCAAC

Reverse complement sequence

GTTGGCTTTAAGATTAATTAATAGTAAGAAGTGAGTCCTATTATTATCCCTGCTCTCAGTGACTGACAGGCAGCTCAACCACATCGATTCGCCACGCAGC[A/G]
ACACCACTTGCACCACCGCCCCTCGTCTCAGCTCATCTCCTCGTCAAACTTCGCTTTCCCCAAAGTCTTCCTCTTCCCTCCTCTCTCTCTCTCTCCCCCA

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	53.90%	45.80%	0.38%	0.00%	NA
All Indica	2759	82.00%	17.50%	0.47%	0.00%	NA
All Japonica	1512	3.40%	96.40%	0.20%	0.00%	NA
Aus	269	40.50%	59.50%	0.00%	0.00%	NA
Indica I	595	94.10%	5.40%	0.50%	0.00%	NA
Indica II	465	56.80%	43.00%	0.22%	0.00%	NA
Indica III	913	85.90%	14.00%	0.11%	0.00%	NA
Indica Intermediate	786	83.30%	15.60%	1.02%	0.00%	NA
Temperate Japonica	767	1.40%	98.60%	0.00%	0.00%	NA
Tropical Japonica	504	6.70%	92.90%	0.40%	0.00%	NA
Japonica Intermediate	241	2.50%	97.10%	0.41%	0.00%	NA
VI/Aromatic	96	87.50%	12.50%	0.00%	0.00%	NA
Intermediate	90	42.20%	55.60%	2.22%	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
vg0701246321	T -> C	LOC_Os07g03180.1	5_prime_UTR_variant ; 210.0bp to feature; MODIFIER	silent_mutation	Average:96.123; most accessible tissue: Callus, score: 98.545	N	N	N	N
vg0701246321	T -> C	LOC_Os07g03190.1	upstream_gene_variant ; 2553.0bp to feature; MODIFIER	silent_mutation	Average:96.123; most accessible tissue: Callus, score: 98.545	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)
vg0701246321	T	C	-0.02	-0.03	-0.02	-0.01	-0.02	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0701246321	NA	2.40E-15	mr1167	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
vg0701246321	NA	1.26E-21	mr1167_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
vg0701246321	NA	9.51E-06	mr1269_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
vg0701246321	NA	5.42E-06	mr1289_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
vg0701246321	NA	6.03E-07	mr1355_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
vg0701246321	NA	6.77E-06	mr1405_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
vg0701246321	NA	4.30E-06	mr1462_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
vg0701246321	NA	1.90E-07	mr1479_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
vg0701246321	NA	4.99E-08	mr1668_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
vg0701246321	NA	1.64E-18	mr1726_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
vg0701246321	NA	5.19E-10	mr1761_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
vg0701246321	NA	1.31E-06	mr1786_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
vg0701246321	NA	5.36E-10	mr1940_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
vg0701246321	NA	8.37E-16	mr1950_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