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Detailed information for vg0900044105:

Variant ID: vg0900044105 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 44105
Reference Allele: G	Alternative Allele: A,T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, T: 0.05, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

TAATGATTTTAGTTGACTTGAACTATGGATTCCGATAATTGTTTCCATCGGCTGCTCTTCCAGATGAGTGAACCATGTTAATGGGAAAAGGATTGCCATT[G/A,T]
ACCTTCATCGGCTTCTTGGAATCATCAAACTTGATTTTGCCCCCCTCAATAGCCAACTGGATCTGTTGTCTAAAAACCTTAGTCATTAGTACAAAGAGAG

Reverse complement sequence

CTCTCTTTGTACTAATGACTAAGGTTTTTAGACAACAGATCCAGTTGGCTATTGAGGGGGGCAAAATCAAGTTTGATGATTCCAAGAAGCCGATGAAGGT[C/T,A]
AATGGCAATCCTTTTCCCATTAACATGGTTCACTCATCTGGAAGAGCAGCCGATGGAAACAATTATCGGAATCCATAGTTCAAGTCAACTAAAATCATTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.70%	28.80%	3.43%	11.89%	A: 0.17%
All Indica	2759	38.10%	45.80%	3.77%	12.11%	A: 0.22%
All Japonica	1512	86.80%	0.30%	1.52%	11.31%	A: 0.07%
Aus	269	66.90%	32.00%	0.00%	1.12%	NA
Indica I	595	47.90%	41.00%	2.35%	8.74%	NA
Indica II	465	47.10%	24.10%	7.53%	21.29%	NA
Indica III	913	30.60%	56.30%	3.29%	9.31%	A: 0.55%
Indica Intermediate	786	34.20%	50.00%	3.18%	12.47%	A: 0.13%
Temperate Japonica	767	75.60%	0.10%	2.61%	21.64%	NA
Tropical Japonica	504	99.40%	0.20%	0.00%	0.40%	NA
Japonica Intermediate	241	96.30%	0.80%	1.24%	1.24%	A: 0.41%
VI/Aromatic	96	20.80%	4.20%	27.08%	46.88%	A: 1.04%
Intermediate	90	73.30%	6.70%	10.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0900044105	G -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900044105	G -> T	LOC_Os09g01002.1	upstream_gene_variant ; 2447.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900044105	G -> T	LOC_Os09g01006.1	downstream_gene_variant ; 747.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900044105	G -> T	LOC_Os09g01006-LOC_Os09g01010	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900044105	G -> A	LOC_Os09g01002.1	upstream_gene_variant ; 2447.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900044105	G -> A	LOC_Os09g01006.1	downstream_gene_variant ; 747.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900044105	G -> A	LOC_Os09g01006-LOC_Os09g01010	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	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)
vg0900044105	G	A	-0.01	-0.01	-0.01	-0.01	-0.01	-0.01
vg0900044105	G	T	-0.01	-0.02	-0.01	-0.01	-0.01	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900044105	4.93E-06	NA	mr1168	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
vg0900044105	1.36E-06	8.80E-08	mr1168	Ind_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
vg0900044105	9.35E-07	7.69E-08	mr1383	Ind_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
vg0900044105	NA	2.09E-13	mr1449	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
vg0900044105	3.55E-06	3.55E-06	mr1449	Ind_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
vg0900044105	NA	1.93E-06	mr1486	Ind_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
vg0900044105	6.05E-06	NA	mr1168_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
vg0900044105	1.66E-06	1.72E-09	mr1168_2	Ind_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
vg0900044105	NA	7.24E-07	mr1486_2	Ind_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