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Detailed information for vg0723871939:

Variant ID: vg0723871939 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 23871939
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.64, G: 0.36, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

ATTCTAGCATTTTCCACATTCATATAGAGGTTAGTGAATCTAGACATATATATCTATATAGATTCACTAACCTCCATATGAATATGGGAAATGCTAAAAT[A/G]
ACTTACATTATGAAACGGATGGAGTACTAATATCTGATATGGAGTAGTGAAAAGATCTGTCAATAGTTTTGTGTTCATGTACGTAGTTGGTCCAAGAAAC

Reverse complement sequence

GTTTCTTGGACCAACTACGTACATGAACACAAAACTATTGACAGATCTTTTCACTACTCCATATCAGATATTAGTACTCCATCCGTTTCATAATGTAAGT[T/C]
ATTTTAGCATTTCCCATATTCATATGGAGGTTAGTGAATCTATATAGATATATATGTCTAGATTCACTAACCTCTATATGAATGTGGAAAATGCTAGAAT

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	53.00%	46.50%	0.08%	0.38%	NA
All Indica	2759	27.00%	72.40%	0.07%	0.47%	NA
All Japonica	1512	99.70%	0.10%	0.07%	0.13%	NA
Aus	269	37.50%	62.50%	0.00%	0.00%	NA
Indica I	595	12.10%	87.60%	0.00%	0.34%	NA
Indica II	465	32.50%	66.50%	0.22%	0.86%	NA
Indica III	913	24.30%	75.50%	0.00%	0.22%	NA
Indica Intermediate	786	38.30%	60.90%	0.13%	0.64%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	0.80%	0.41%	0.41%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	67.80%	27.80%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0723871939	A -> DEL	N	N	silent_mutation	Average:67.634; most accessible tissue: Minghui63 root, score: 96.917	N	N	N	N
vg0723871939	A -> G	LOC_Os07g39820.1	downstream_gene_variant ; 794.0bp to feature; MODIFIER	silent_mutation	Average:67.634; most accessible tissue: Minghui63 root, score: 96.917	N	N	N	N
vg0723871939	A -> G	LOC_Os07g39820-LOC_Os07g39830	intergenic_region ; MODIFIER	silent_mutation	Average:67.634; most accessible tissue: Minghui63 root, score: 96.917	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)
vg0723871939	A	G	-0.04	0.04	0.0	-0.01	0.01	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0723871939	3.63E-06	3.63E-06	mr1175	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
vg0723871939	NA	5.53E-08	mr1215_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
vg0723871939	NA	3.01E-07	mr1215_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
vg0723871939	NA	6.10E-10	mr1218_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
vg0723871939	NA	7.64E-09	mr1220_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
vg0723871939	NA	1.00E-07	mr1220_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
vg0723871939	NA	4.59E-07	mr1422_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
vg0723871939	NA	2.22E-14	mr1521_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
vg0723871939	NA	3.93E-06	mr1521_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
vg0723871939	NA	2.29E-07	mr1583_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
vg0723871939	8.62E-06	6.19E-11	mr1607_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
vg0723871939	NA	2.11E-06	mr1607_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
vg0723871939	NA	8.33E-11	mr1646_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