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Detailed information for vg0235186964:

Variant ID: vg0235186964 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 35186964
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

TACTCCTACTACCGCTATATGAAGTGGTATATATTTATTATTTTATTTTAATGGTGACAGAGAGGATACACGTGGACACATTACTATACACGTAAACCAC[A/C]
AAGATTTACCATTTCCATCCTATAAAAAACCTAATACTTGTGTGTCCAGGTTCAATGCTAGAAATAATTTTTTTAAGGGCAGAGAAGTATGACTATCGTC

Reverse complement sequence

GACGATAGTCATACTTCTCTGCCCTTAAAAAAATTATTTCTAGCATTGAACCTGGACACACAAGTATTAGGTTTTTTATAGGATGGAAATGGTAAATCTT[T/G]
GTGGTTTACGTGTATAGTAATGTGTCCACGTGTATCCTCTCTGTCACCATTAAAATAAAATAATAAATATATACCACTTCATATAGCGGTAGTAGGAGTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.30%	41.30%	0.40%	0.00%	NA
All Indica	2759	45.50%	53.80%	0.69%	0.00%	NA
All Japonica	1512	74.70%	25.30%	0.00%	0.00%	NA
Aus	269	85.10%	14.90%	0.00%	0.00%	NA
Indica I	595	42.90%	56.10%	1.01%	0.00%	NA
Indica II	465	23.70%	75.50%	0.86%	0.00%	NA
Indica III	913	54.50%	45.00%	0.44%	0.00%	NA
Indica Intermediate	786	49.90%	49.50%	0.64%	0.00%	NA
Temperate Japonica	767	91.80%	8.20%	0.00%	0.00%	NA
Tropical Japonica	504	56.50%	43.50%	0.00%	0.00%	NA
Japonica Intermediate	241	58.50%	41.50%	0.00%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	61.10%	38.90%	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
vg0235186964	A -> C	LOC_Os02g57410.1	upstream_gene_variant ; 2806.0bp to feature; MODIFIER	silent_mutation	Average:97.141; most accessible tissue: Minghui63 flag leaf, score: 99.2	N	N	N	N
vg0235186964	A -> C	LOC_Os02g57410.3	upstream_gene_variant ; 2806.0bp to feature; MODIFIER	silent_mutation	Average:97.141; most accessible tissue: Minghui63 flag leaf, score: 99.2	N	N	N	N
vg0235186964	A -> C	LOC_Os02g57410.5	upstream_gene_variant ; 2806.0bp to feature; MODIFIER	silent_mutation	Average:97.141; most accessible tissue: Minghui63 flag leaf, score: 99.2	N	N	N	N
vg0235186964	A -> C	LOC_Os02g57410.6	upstream_gene_variant ; 2806.0bp to feature; MODIFIER	silent_mutation	Average:97.141; most accessible tissue: Minghui63 flag leaf, score: 99.2	N	N	N	N
vg0235186964	A -> C	LOC_Os02g57410.7	upstream_gene_variant ; 2806.0bp to feature; MODIFIER	silent_mutation	Average:97.141; most accessible tissue: Minghui63 flag leaf, score: 99.2	N	N	N	N
vg0235186964	A -> C	LOC_Os02g57410.8	upstream_gene_variant ; 2806.0bp to feature; MODIFIER	silent_mutation	Average:97.141; most accessible tissue: Minghui63 flag leaf, score: 99.2	N	N	N	N
vg0235186964	A -> C	LOC_Os02g57410.9	upstream_gene_variant ; 2806.0bp to feature; MODIFIER	silent_mutation	Average:97.141; most accessible tissue: Minghui63 flag leaf, score: 99.2	N	N	N	N
vg0235186964	A -> C	LOC_Os02g57410.10	upstream_gene_variant ; 2806.0bp to feature; MODIFIER	silent_mutation	Average:97.141; most accessible tissue: Minghui63 flag leaf, score: 99.2	N	N	N	N
vg0235186964	A -> C	LOC_Os02g57410.4	upstream_gene_variant ; 2806.0bp to feature; MODIFIER	silent_mutation	Average:97.141; most accessible tissue: Minghui63 flag leaf, score: 99.2	N	N	N	N
vg0235186964	A -> C	LOC_Os02g57410.2	upstream_gene_variant ; 2806.0bp to feature; MODIFIER	silent_mutation	Average:97.141; most accessible tissue: Minghui63 flag leaf, score: 99.2	N	N	N	N
vg0235186964	A -> C	LOC_Os02g57420.1	downstream_gene_variant ; 3429.0bp to feature; MODIFIER	silent_mutation	Average:97.141; most accessible tissue: Minghui63 flag leaf, score: 99.2	N	N	N	N
vg0235186964	A -> C	LOC_Os02g57410-LOC_Os02g57420	intergenic_region ; MODIFIER	silent_mutation	Average:97.141; most accessible tissue: Minghui63 flag leaf, score: 99.2	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)
vg0235186964	A	C	0.01	0.0	-0.01	0.0	0.0	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0235186964	9.33E-06	NA	mr1188	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
vg0235186964	NA	2.12E-07	mr1125_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
vg0235186964	2.68E-06	1.58E-12	mr1188_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
vg0235186964	NA	8.94E-09	mr1526_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
vg0235186964	NA	9.43E-08	mr1798_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