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Detailed information for vg0435422369:

Variant ID: vg0435422369 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 35422369
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAGGATGTTGGCTCTTATGCAAGAGCTAGCTTAACACAAACTCCTAGGTAAATACATTAAATGCATAGGTGAGAGATAGAGAGAGAGGAGAAGAAAGTT[G/A]
TAGCCAACCTTATAGCTAATCCATTATATATGTTAGCTTTAAGATAGACTAATAGTGGTGAGCTCTACTATTATCCTTGCTCTTGCTCTTAGTAGTACTA

Reverse complement sequence

TAGTACTACTAAGAGCAAGAGCAAGGATAATAGTAGAGCTCACCACTATTAGTCTATCTTAAAGCTAACATATATAATGGATTAGCTATAAGGTTGGCTA[C/T]
AACTTTCTTCTCCTCTCTCTCTATCTCTCACCTATGCATTTAATGTATTTACCTAGGAGTTTGTGTTAAGCTAGCTCTTGCATAAGAGCCAACATCCTTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.90%	0.70%	0.47%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.04%	0.00%	NA
All Japonica	1512	96.60%	2.00%	1.39%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	95.80%	2.90%	1.30%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	93.40%	2.50%	4.15%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0435422369	G -> A	LOC_Os04g59550.1	upstream_gene_variant ; 826.0bp to feature; MODIFIER	silent_mutation	Average:84.726; most accessible tissue: Zhenshan97 root, score: 95.289	N	N	N	N
vg0435422369	G -> A	LOC_Os04g59570.1	upstream_gene_variant ; 4595.0bp to feature; MODIFIER	silent_mutation	Average:84.726; most accessible tissue: Zhenshan97 root, score: 95.289	N	N	N	N
vg0435422369	G -> A	LOC_Os04g59550.4	upstream_gene_variant ; 826.0bp to feature; MODIFIER	silent_mutation	Average:84.726; most accessible tissue: Zhenshan97 root, score: 95.289	N	N	N	N
vg0435422369	G -> A	LOC_Os04g59550.2	upstream_gene_variant ; 817.0bp to feature; MODIFIER	silent_mutation	Average:84.726; most accessible tissue: Zhenshan97 root, score: 95.289	N	N	N	N
vg0435422369	G -> A	LOC_Os04g59550.3	upstream_gene_variant ; 817.0bp to feature; MODIFIER	silent_mutation	Average:84.726; most accessible tissue: Zhenshan97 root, score: 95.289	N	N	N	N
vg0435422369	G -> A	LOC_Os04g59550.5	upstream_gene_variant ; 817.0bp to feature; MODIFIER	silent_mutation	Average:84.726; most accessible tissue: Zhenshan97 root, score: 95.289	N	N	N	N
vg0435422369	G -> A	LOC_Os04g59570.2	upstream_gene_variant ; 4595.0bp to feature; MODIFIER	silent_mutation	Average:84.726; most accessible tissue: Zhenshan97 root, score: 95.289	N	N	N	N
vg0435422369	G -> A	LOC_Os04g59540.1	downstream_gene_variant ; 3527.0bp to feature; MODIFIER	silent_mutation	Average:84.726; most accessible tissue: Zhenshan97 root, score: 95.289	N	N	N	N
vg0435422369	G -> A	LOC_Os04g59560.1	downstream_gene_variant ; 617.0bp to feature; MODIFIER	silent_mutation	Average:84.726; most accessible tissue: Zhenshan97 root, score: 95.289	N	N	N	N
vg0435422369	G -> A	LOC_Os04g59550-LOC_Os04g59560	intergenic_region ; MODIFIER	silent_mutation	Average:84.726; most accessible tissue: Zhenshan97 root, score: 95.289	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)
vg0435422369	G	A	-0.01	0.02	0.0	0.02	0.0	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0435422369	5.61E-07	NA	mr1719	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