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Detailed information for vg0800324457:

Variant ID: vg0800324457 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 324457
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, A: 0.05, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

TCAATAAGTCCATCGATGAGAGAATTAGCGTCAAGATATGTTCATCACCTATCTTGCTTATCGGGACATGTACAATTAATCCATGTATGTGCATGTATGG[T/A]
ACGTACTACCAACAAGTACTCCATATAATTGTAGTGCAAACAGCTAATAGTAGTTAGTCCTAAGTTAGGTAGATAGGTAGGTAGATTAGGCAGCATATAT

Reverse complement sequence

ATATATGCTGCCTAATCTACCTACCTATCTACCTAACTTAGGACTAACTACTATTAGCTGTTTGCACTACAATTATATGGAGTACTTGTTGGTAGTACGT[A/T]
CCATACATGCACATACATGGATTAATTGTACATGTCCCGATAAGCAAGATAGGTGATGAACATATCTTGACGCTAATTCTCTCATCGATGGACTTATTGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.00%	25.60%	0.23%	0.17%	NA
All Indica	2759	62.50%	36.90%	0.33%	0.29%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	65.10%	34.60%	0.37%	0.00%	NA
Indica I	595	68.10%	31.30%	0.17%	0.50%	NA
Indica II	465	86.20%	13.50%	0.22%	0.00%	NA
Indica III	913	41.90%	57.50%	0.22%	0.33%	NA
Indica Intermediate	786	68.10%	31.00%	0.64%	0.25%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	15.60%	83.30%	1.04%	0.00%	NA
Intermediate	90	82.20%	17.80%	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
vg0800324457	T -> A	LOC_Os08g01530.1	upstream_gene_variant ; 1457.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0800324457	T -> A	LOC_Os08g01540.1	upstream_gene_variant ; 1537.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0800324457	T -> A	LOC_Os08g01550.1	upstream_gene_variant ; 4417.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0800324457	T -> A	LOC_Os08g01520.1	downstream_gene_variant ; 3445.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0800324457	T -> A	LOC_Os08g01530-LOC_Os08g01540	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0800324457	T -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	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)
vg0800324457	T	A	-0.04	-0.03	-0.03	-0.04	-0.03	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0800324457	1.09E-10	4.03E-17	mr1277	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
vg0800324457	2.19E-10	7.41E-14	mr1277	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
vg0800324457	NA	6.38E-07	mr1705	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
vg0800324457	4.71E-18	1.11E-32	mr1746	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
vg0800324457	1.55E-16	4.50E-22	mr1746	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
vg0800324457	2.68E-11	6.95E-21	mr1277_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
vg0800324457	2.24E-10	3.00E-12	mr1277_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
vg0800324457	8.18E-07	2.33E-08	mr1403_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
vg0800324457	NA	3.74E-09	mr1705_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
vg0800324457	1.61E-23	5.45E-44	mr1746_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
vg0800324457	4.96E-20	1.36E-26	mr1746_2	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