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Detailed information for vg0803364457:

Variant ID: vg0803364457 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 3364457
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

CTTGGATGGTGATAGTGATACACTGGTGTTTGTAGCTGCTACATCAAACTGAATGAAACTGAATTTGAAGTAACAATTCAAATAGGAATGTGATTCCTTA[T/C]
GACTCTTCAGCTGTATAAGATAATTCATTGTTGAAACCCTATTAAGTGTTATTGCCTTTTAGCGACCTCACCTCACTTCAATTTGTTTGATTGTGAACTT

Reverse complement sequence

AAGTTCACAATCAAACAAATTGAAGTGAGGTGAGGTCGCTAAAAGGCAATAACACTTAATAGGGTTTCAACAATGAATTATCTTATACAGCTGAAGAGTC[A/G]
TAAGGAATCACATTCCTATTTGAATTGTTACTTCAAATTCAGTTTCATTCAGTTTGATGTAGCAGCTACAAACACCAGTGTATCACTATCACCATCCAAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.70%	14.30%	0.00%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	55.90%	44.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	27.80%	72.20%	0.00%	0.00%	NA
Tropical Japonica	504	90.90%	9.10%	0.00%	0.00%	NA
Japonica Intermediate	241	72.20%	27.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0803364457	T -> C	LOC_Os08g06110.2	upstream_gene_variant ; 1462.0bp to feature; MODIFIER	silent_mutation	Average:59.444; most accessible tissue: Minghui63 flag leaf, score: 90.43	N	N	N	N
vg0803364457	T -> C	LOC_Os08g06110.3	upstream_gene_variant ; 1273.0bp to feature; MODIFIER	silent_mutation	Average:59.444; most accessible tissue: Minghui63 flag leaf, score: 90.43	N	N	N	N
vg0803364457	T -> C	LOC_Os08g06110.5	upstream_gene_variant ; 1419.0bp to feature; MODIFIER	silent_mutation	Average:59.444; most accessible tissue: Minghui63 flag leaf, score: 90.43	N	N	N	N
vg0803364457	T -> C	LOC_Os08g06110.4	upstream_gene_variant ; 1471.0bp to feature; MODIFIER	silent_mutation	Average:59.444; most accessible tissue: Minghui63 flag leaf, score: 90.43	N	N	N	N
vg0803364457	T -> C	LOC_Os08g06100-LOC_Os08g06110	intergenic_region ; MODIFIER	silent_mutation	Average:59.444; most accessible tissue: Minghui63 flag leaf, score: 90.43	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)
vg0803364457	T	C	0.01	0.02	0.02	0.01	0.01	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0803364457	NA	1.15E-09	Heading_date	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0803364457	NA	2.91E-11	Plant_height	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0803364457	NA	7.25E-17	Spikelet_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0803364457	NA	9.83E-13	Spikelet_length	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0803364457	NA	1.58E-06	mr1011	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
vg0803364457	NA	9.28E-08	mr1252	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
vg0803364457	NA	7.39E-08	mr1252	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
vg0803364457	NA	4.74E-06	mr1561	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
vg0803364457	NA	4.00E-06	mr1788	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
vg0803364457	2.80E-06	2.80E-06	mr1935	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
vg0803364457	NA	1.32E-07	mr1748_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