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Detailed information for vg0810145472:

Variant ID: vg0810145472 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 10145472
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.89, C: 0.13, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

TGCTATACTACTCCCTCCATTTCATAATGTAAGACTTTCTAGCATTGCTCATATTCATATACTCTCTCCATTTCAAAATATAAGTCATTTTAGCATTTCT[T/C]
ATATTCATATATATCTAGATTCATTAACATCAACATGAATGTGGAAAATGTTAGAGTGACTTACATTGTGAAACGGAGGGAGTAGATGTTAATGAATCTA

Reverse complement sequence

TAGATTCATTAACATCTACTCCCTCCGTTTCACAATGTAAGTCACTCTAACATTTTCCACATTCATGTTGATGTTAATGAATCTAGATATATATGAATAT[A/G]
AGAAATGCTAAAATGACTTATATTTTGAAATGGAGAGAGTATATGAATATGAGCAATGCTAGAAAGTCTTACATTATGAAATGGAGGGAGTAGTATAGCA

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	86.90%	13.10%	0.02%	0.00%	NA
All Indica	2759	97.90%	2.10%	0.04%	0.00%	NA
All Japonica	1512	64.20%	35.80%	0.00%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	95.30%	4.50%	0.17%	0.00%	NA
Indica II	465	96.60%	3.40%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	98.50%	1.50%	0.00%	0.00%	NA
Temperate Japonica	767	38.20%	61.80%	0.00%	0.00%	NA
Tropical Japonica	504	92.90%	7.10%	0.00%	0.00%	NA
Japonica Intermediate	241	86.70%	13.30%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	80.00%	20.00%	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
vg0810145472	T -> C	LOC_Os08g16580.1	upstream_gene_variant ; 695.0bp to feature; MODIFIER	silent_mutation	Average:78.339; most accessible tissue: Minghui63 flower, score: 87.086	N	N	N	N
vg0810145472	T -> C	LOC_Os08g16570.1	downstream_gene_variant ; 3747.0bp to feature; MODIFIER	silent_mutation	Average:78.339; most accessible tissue: Minghui63 flower, score: 87.086	N	N	N	N
vg0810145472	T -> C	LOC_Os08g16590.1	downstream_gene_variant ; 2442.0bp to feature; MODIFIER	silent_mutation	Average:78.339; most accessible tissue: Minghui63 flower, score: 87.086	N	N	N	N
vg0810145472	T -> C	LOC_Os08g16570.3	downstream_gene_variant ; 3747.0bp to feature; MODIFIER	silent_mutation	Average:78.339; most accessible tissue: Minghui63 flower, score: 87.086	N	N	N	N
vg0810145472	T -> C	LOC_Os08g16580-LOC_Os08g16590	intergenic_region ; MODIFIER	silent_mutation	Average:78.339; most accessible tissue: Minghui63 flower, score: 87.086	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)
vg0810145472	T	C	0.0	0.02	0.02	0.0	0.01	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0810145472	NA	3.32E-06	mr1057	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
vg0810145472	NA	1.89E-12	mr1182	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
vg0810145472	NA	1.53E-07	mr1182	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
vg0810145472	NA	2.86E-06	mr1282	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
vg0810145472	NA	2.34E-06	mr1330	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
vg0810145472	NA	1.86E-07	mr1627	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
vg0810145472	NA	5.24E-06	mr1650	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
vg0810145472	5.41E-10	1.17E-09	mr1057_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
vg0810145472	NA	6.46E-11	mr1057_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
vg0810145472	NA	1.32E-06	mr1627_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