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Detailed information for vg0203536993:

Variant ID: vg0203536993 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 3536993
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAATTAATCTATTCGTTTTTCAAATAGCTAATACTTAATTAATCACGCACTAATGGACCGCTCCGTTTTTCGTGTGGAGGGAATAAGTTCCCATTCACC[A/G]
TATGCGAACACAGTGTAATGGGACATCATCAATGTTACTATACCATCATATTGAACCATGGCTTCAATGATATTGGTGTCGTGAAAAGATCTATTTTTGA

Reverse complement sequence

TCAAAAATAGATCTTTTCACGACACCAATATCATTGAAGCCATGGTTCAATATGATGGTATAGTAACATTGATGATGTCCCATTACACTGTGTTCGCATA[T/C]
GGTGAATGGGAACTTATTCCCTCCACACGAAAAACGGAGCGGTCCATTAGTGCGTGATTAATTAAGTATTAGCTATTTGAAAAACGAATAGATTAATTTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.90%	10.60%	1.52%	0.00%	NA
All Indica	2759	97.00%	2.20%	0.76%	0.00%	NA
All Japonica	1512	74.60%	22.40%	2.98%	0.00%	NA
Aus	269	79.20%	20.40%	0.37%	0.00%	NA
Indica I	595	98.70%	0.50%	0.84%	0.00%	NA
Indica II	465	98.90%	0.20%	0.86%	0.00%	NA
Indica III	913	96.30%	3.60%	0.11%	0.00%	NA
Indica Intermediate	786	95.40%	3.20%	1.40%	0.00%	NA
Temperate Japonica	767	96.00%	0.90%	3.13%	0.00%	NA
Tropical Japonica	504	35.30%	61.50%	3.17%	0.00%	NA
Japonica Intermediate	241	88.80%	9.10%	2.07%	0.00%	NA
VI/Aromatic	96	72.90%	25.00%	2.08%	0.00%	NA
Intermediate	90	75.60%	21.10%	3.33%	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
vg0203536993	A -> G	LOC_Os02g06960.1	upstream_gene_variant ; 3940.0bp to feature; MODIFIER	silent_mutation	Average:89.8; most accessible tissue: Zhenshan97 panicle, score: 97.067	N	N	N	N
vg0203536993	A -> G	LOC_Os02g06950-LOC_Os02g06960	intergenic_region ; MODIFIER	silent_mutation	Average:89.8; most accessible tissue: Zhenshan97 panicle, score: 97.067	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)
vg0203536993	A	G	0.0	0.01	0.0	0.0	0.0	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0203536993	NA	8.74E-07	mr1248	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
vg0203536993	NA	8.88E-06	mr1740	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
vg0203536993	NA	1.52E-07	mr1308_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
vg0203536993	NA	3.26E-10	mr1398_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
vg0203536993	NA	2.92E-07	mr1398_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
vg0203536993	NA	3.63E-07	mr1401_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
vg0203536993	NA	9.58E-09	mr1606_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
vg0203536993	NA	1.33E-06	mr1905_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