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Detailed information for vg0915237973:

Variant ID: vg0915237973 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 15237973
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

CCGGAGAAAGCGAGCTAGCAAAGCAGAGCGCAAAAAGCAAAGCGTTGGGAGATAGAGTAGTTTTTTTAGTAGAGGAATAAGTTCAGATTTACTCCCTTAA[C/T]
TAGTGTGAAAAGTTTCCGAATGAGAGGGAGAAAAGTGGCCCTCACATTTTTCTAATGAATGACAAATGGGTCTATATATATATATATCTTCAATTTTAAT

Reverse complement sequence

ATTAAAATTGAAGATATATATATATATAGACCCATTTGTCATTCATTAGAAAAATGTGAGGGCCACTTTTCTCCCTCTCATTCGGAAACTTTTCACACTA[G/A]
TTAAGGGAGTAAATCTGAACTTATTCCTCTACTAAAAAAACTACTCTATCTCCCAACGCTTTGCTTTTTGCGCTCTGCTTTGCTAGCTCGCTTTCTCCGG

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	79.80%	20.10%	0.11%	0.00%	NA
All Indica	2759	65.90%	33.90%	0.14%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	66.20%	33.60%	0.17%	0.00%	NA
Indica II	465	46.00%	54.00%	0.00%	0.00%	NA
Indica III	913	76.20%	23.70%	0.11%	0.00%	NA
Indica Intermediate	786	65.50%	34.20%	0.25%	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	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	12.20%	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
vg0915237973	C -> T	LOC_Os09g25420.1	upstream_gene_variant ; 149.0bp to feature; MODIFIER	silent_mutation	Average:87.016; most accessible tissue: Zhenshan97 panicle, score: 92.904	N	N	N	N
vg0915237973	C -> T	LOC_Os09g25410.1	downstream_gene_variant ; 1969.0bp to feature; MODIFIER	silent_mutation	Average:87.016; most accessible tissue: Zhenshan97 panicle, score: 92.904	N	N	N	N
vg0915237973	C -> T	LOC_Os09g25430.1	downstream_gene_variant ; 2473.0bp to feature; MODIFIER	silent_mutation	Average:87.016; most accessible tissue: Zhenshan97 panicle, score: 92.904	N	N	N	N
vg0915237973	C -> T	LOC_Os09g25410.2	downstream_gene_variant ; 1969.0bp to feature; MODIFIER	silent_mutation	Average:87.016; most accessible tissue: Zhenshan97 panicle, score: 92.904	N	N	N	N
vg0915237973	C -> T	LOC_Os09g25420-LOC_Os09g25430	intergenic_region ; MODIFIER	silent_mutation	Average:87.016; most accessible tissue: Zhenshan97 panicle, score: 92.904	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)
vg0915237973	C	T	-0.06	-0.07	-0.05	-0.07	-0.05	-0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0915237973	NA	2.51E-06	mr1004	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
vg0915237973	NA	6.85E-08	mr1006	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
vg0915237973	NA	3.37E-06	mr1007	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
vg0915237973	NA	9.29E-09	mr1007	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
vg0915237973	NA	3.48E-08	mr1052	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
vg0915237973	NA	1.82E-08	mr1707	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
vg0915237973	NA	2.19E-08	mr1728	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
vg0915237973	8.58E-06	2.96E-08	mr1006_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
vg0915237973	NA	1.85E-09	mr1006_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
vg0915237973	NA	5.99E-06	mr1010_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
vg0915237973	NA	7.86E-06	mr1051_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
vg0915237973	NA	7.82E-06	mr1294_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
vg0915237973	NA	5.60E-06	mr1497_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
vg0915237973	NA	8.82E-06	mr1705_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
vg0915237973	NA	1.02E-10	mr1707_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
vg0915237973	NA	4.92E-12	mr1728_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