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Detailed information for vg0509256609:

Variant ID: vg0509256609 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 9256609
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATCATCGTCTCCGTGTGTGTCGTCGTCGTTGTGTCGTAGCTGCTTGCCGTGCCGCTGCTGCGCGTGTGCCGGCTGAGCCGCTTAGCTGCAGCTGCTTGC[C/A]
GCTTTGCCACAGCCGCAGCCGTGCCGGTTGCGTTTTTGCTCGCAGCCCTGCTGCTCTAGCCGTGCATGGTCGCTACTGGCTGTGCCGTCACCCTAACCCT

Reverse complement sequence

AGGGTTAGGGTGACGGCACAGCCAGTAGCGACCATGCACGGCTAGAGCAGCAGGGCTGCGAGCAAAAACGCAACCGGCACGGCTGCGGCTGTGGCAAAGC[G/T]
GCAAGCAGCTGCAGCTAAGCGGCTCAGCCGGCACACGCGCAGCAGCGGCACGGCAAGCAGCTACGACACAACGACGACGACACACACGGAGACGATGATG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.80%	0.10%	5.71%	2.39%	NA
All Indica	2759	94.90%	0.00%	4.49%	0.54%	NA
All Japonica	1512	85.40%	0.20%	9.19%	5.22%	NA
Aus	269	92.90%	0.70%	0.37%	5.95%	NA
Indica I	595	85.50%	0.00%	14.29%	0.17%	NA
Indica II	465	97.60%	0.20%	1.29%	0.86%	NA
Indica III	913	99.70%	0.00%	0.11%	0.22%	NA
Indica Intermediate	786	94.90%	0.00%	4.07%	1.02%	NA
Temperate Japonica	767	76.30%	0.40%	13.82%	9.52%	NA
Tropical Japonica	504	97.20%	0.00%	2.58%	0.20%	NA
Japonica Intermediate	241	89.60%	0.00%	8.30%	2.07%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	0.00%	6.67%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0509256609	C -> DEL	N	N	silent_mutation	Average:79.553; most accessible tissue: Zhenshan97 flag leaf, score: 93.448	N	N	N	N
vg0509256609	C -> A	LOC_Os05g16350.1	upstream_gene_variant ; 4026.0bp to feature; MODIFIER	silent_mutation	Average:79.553; most accessible tissue: Zhenshan97 flag leaf, score: 93.448	N	N	N	N
vg0509256609	C -> A	LOC_Os05g16330.1	downstream_gene_variant ; 4949.0bp to feature; MODIFIER	silent_mutation	Average:79.553; most accessible tissue: Zhenshan97 flag leaf, score: 93.448	N	N	N	N
vg0509256609	C -> A	LOC_Os05g16340.1	downstream_gene_variant ; 2009.0bp to feature; MODIFIER	silent_mutation	Average:79.553; most accessible tissue: Zhenshan97 flag leaf, score: 93.448	N	N	N	N
vg0509256609	C -> A	LOC_Os05g16340-LOC_Os05g16350	intergenic_region ; MODIFIER	silent_mutation	Average:79.553; most accessible tissue: Zhenshan97 flag leaf, score: 93.448	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)
vg0509256609	C	A	0.01	0.0	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
vg0509256609	NA	5.41E-06	mr1071_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
vg0509256609	3.29E-06	3.66E-06	mr1203_2	Jap_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
vg0509256609	1.36E-07	2.82E-06	mr1613_2	Jap_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
vg0509256609	NA	3.89E-06	mr1619_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
vg0509256609	5.19E-06	5.77E-06	mr1913_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