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Detailed information for vg0626294821:

Variant ID: vg0626294821 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 26294821
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

AAAACAGGGGGCGAAAAATGTACTATGTGATTAGGGCGTTCACGGTGGACTTACGTGACGTTCAGCCTCGCCCTCCCTAGTCTGCAAAGGAAAAAGCACA[C/T]
GCCACGTTTGCTTCTGGGCCCAAAAAAAAGTTTTTGTGTCCAAAGTTTGCCACCGGGTTCTTGGAAGAAGCTACTCATTTGTGTGGAGAGAAGCTAATAG

Reverse complement sequence

CTATTAGCTTCTCTCCACACAAATGAGTAGCTTCTTCCAAGAACCCGGTGGCAAACTTTGGACACAAAAACTTTTTTTTGGGCCCAGAAGCAAACGTGGC[G/A]
TGTGCTTTTTCCTTTGCAGACTAGGGAGGGCGAGGCTGAACGTCACGTAAGTCCACCGTGAACGCCCTAATCACATAGTACATTTTTCGCCCCCTGTTTT

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	79.90%	20.00%	0.11%	0.00%	NA
All Indica	2759	66.10%	33.70%	0.18%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	88.20%	11.60%	0.17%	0.00%	NA
Indica II	465	44.10%	55.90%	0.00%	0.00%	NA
Indica III	913	59.00%	40.60%	0.33%	0.00%	NA
Indica Intermediate	786	70.60%	29.30%	0.13%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0626294821	C -> T	LOC_Os06g43680.1	upstream_gene_variant ; 1858.0bp to feature; MODIFIER	silent_mutation	Average:76.868; most accessible tissue: Zhenshan97 root, score: 87.281	N	N	N	N
vg0626294821	C -> T	LOC_Os06g43670.1	downstream_gene_variant ; 2476.0bp to feature; MODIFIER	silent_mutation	Average:76.868; most accessible tissue: Zhenshan97 root, score: 87.281	N	N	N	N
vg0626294821	C -> T	LOC_Os06g43670-LOC_Os06g43680	intergenic_region ; MODIFIER	silent_mutation	Average:76.868; most accessible tissue: Zhenshan97 root, score: 87.281	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)
vg0626294821	C	T	-0.1	-0.05	-0.04	-0.01	-0.05	-0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0626294821	NA	1.57E-06	mr1051	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
vg0626294821	NA	7.73E-06	mr1170	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
vg0626294821	NA	2.04E-07	mr1378	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
vg0626294821	NA	3.97E-06	mr1378	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
vg0626294821	NA	4.19E-08	mr1536	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
vg0626294821	NA	1.42E-06	mr1568	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
vg0626294821	NA	4.51E-06	mr1749	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
vg0626294821	NA	1.75E-06	mr1310_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
vg0626294821	NA	7.00E-10	mr1498_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
vg0626294821	NA	5.25E-07	mr1498_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
vg0626294821	NA	1.57E-06	mr1536_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
vg0626294821	3.91E-06	NA	mr1795_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
vg0626294821	NA	8.56E-06	mr1942_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
vg0626294821	NA	5.59E-07	mr1974_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