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Detailed information for vg0131565701:

Variant ID: vg0131565701 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 31565701
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

CTTGCCGAAGATCGTCAACGGTCGCGCAATCTACGTGTTTTTTTTCTTTTTCCTTTTCCCCTTCCCTTTTGTTCTTTTGATCAGGAATCGAACTATCGAT[G/A]
CTCCCAATGTTAATGGTCTAACAGGCCGACAGGGAAGAGCCTATTACCGATTGCGCGCTCCACTGGGTTTGATAGTGCGACACATATATATAACCTTAAA

Reverse complement sequence

TTTAAGGTTATATATATGTGTCGCACTATCAAACCCAGTGGAGCGCGCAATCGGTAATAGGCTCTTCCCTGTCGGCCTGTTAGACCATTAACATTGGGAG[C/T]
ATCGATAGTTCGATTCCTGATCAAAAGAACAAAAGGGAAGGGGAAAAGGAAAAAGAAAAAAAACACGTAGATTGCGCGACCGTTGACGATCTTCGGCAAG

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	65.90%	34.10%	0.00%	0.00%	NA
All Indica	2759	98.00%	2.00%	0.00%	0.00%	NA
All Japonica	1512	7.40%	92.60%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	96.80%	3.20%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	96.10%	3.90%	0.00%	0.00%	NA
Temperate Japonica	767	9.10%	90.90%	0.00%	0.00%	NA
Tropical Japonica	504	6.30%	93.70%	0.00%	0.00%	NA
Japonica Intermediate	241	4.10%	95.90%	0.00%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	31.10%	68.90%	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
vg0131565701	G -> A	LOC_Os01g54870.1	upstream_gene_variant ; 4865.0bp to feature; MODIFIER	silent_mutation	Average:86.75; most accessible tissue: Callus, score: 97.125	N	N	N	N
vg0131565701	G -> A	LOC_Os01g54880.1	upstream_gene_variant ; 1535.0bp to feature; MODIFIER	silent_mutation	Average:86.75; most accessible tissue: Callus, score: 97.125	N	N	N	N
vg0131565701	G -> A	LOC_Os01g54890.1	upstream_gene_variant ; 2190.0bp to feature; MODIFIER	silent_mutation	Average:86.75; most accessible tissue: Callus, score: 97.125	N	N	N	N
vg0131565701	G -> A	LOC_Os01g54900.1	downstream_gene_variant ; 3207.0bp to feature; MODIFIER	silent_mutation	Average:86.75; most accessible tissue: Callus, score: 97.125	N	N	N	N
vg0131565701	G -> A	LOC_Os01g54880-LOC_Os01g54890	intergenic_region ; MODIFIER	silent_mutation	Average:86.75; most accessible tissue: Callus, score: 97.125	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)
vg0131565701	G	A	0.0	0.01	0.01	-0.01	-0.02	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0131565701	NA	9.37E-13	mr1010	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
vg0131565701	NA	3.39E-15	mr1062	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
vg0131565701	NA	1.02E-10	mr1325	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
vg0131565701	NA	2.27E-06	mr1527	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
vg0131565701	NA	2.60E-12	mr1553	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
vg0131565701	NA	2.78E-08	mr1781	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
vg0131565701	NA	1.13E-06	mr1979	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
vg0131565701	3.54E-06	8.81E-25	mr1010_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
vg0131565701	NA	7.77E-13	mr1035_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
vg0131565701	NA	3.30E-27	mr1051_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
vg0131565701	NA	1.86E-06	mr1227_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
vg0131565701	NA	1.08E-12	mr1553_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