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Detailed information for vg0507847236:

Variant ID: vg0507847236 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7847236
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.73, A: 0.27, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

AATTTGTCATAAGTGGCAAAAAGCAAACGTCACAGATTTATATAATGCATTTCCAGAAAAATATATTAAAAGGTGAAGCAATTTAATCAAGTGAATTAAC[A/G]
AGGAAACTAAAATTTTCCTTTAAAAATCATGGCTGAAAATATTTTTGTAATATTCTGCATGTTCTAAATTATTCTCTGAAATTTTCCGTGAAATTTAGGC

Reverse complement sequence

GCCTAAATTTCACGGAAAATTTCAGAGAATAATTTAGAACATGCAGAATATTACAAAAATATTTTCAGCCATGATTTTTAAAGGAAAATTTTAGTTTCCT[T/C]
GTTAATTCACTTGATTAAATTGCTTCACCTTTTAATATATTTTTCTGGAAATGCATTATATAAATCTGTGACGTTTGCTTTTTGCCACTTATGACAAATT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.20%	41.70%	0.11%	0.00%	NA
All Indica	2759	87.10%	12.90%	0.07%	0.00%	NA
All Japonica	1512	3.20%	96.80%	0.00%	0.00%	NA
Aus	269	97.00%	3.00%	0.00%	0.00%	NA
Indica I	595	97.30%	2.70%	0.00%	0.00%	NA
Indica II	465	69.20%	30.50%	0.22%	0.00%	NA
Indica III	913	90.50%	9.50%	0.00%	0.00%	NA
Indica Intermediate	786	85.90%	14.00%	0.13%	0.00%	NA
Temperate Japonica	767	4.00%	96.00%	0.00%	0.00%	NA
Tropical Japonica	504	2.40%	97.60%	0.00%	0.00%	NA
Japonica Intermediate	241	2.50%	97.50%	0.00%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	43.30%	53.30%	3.33%	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
vg0507847236	A -> G	LOC_Os05g14034.1	upstream_gene_variant ; 957.0bp to feature; MODIFIER	silent_mutation	Average:81.119; most accessible tissue: Minghui63 young leaf, score: 89.557	N	N	N	N
vg0507847236	A -> G	LOC_Os05g14040.1	downstream_gene_variant ; 2611.0bp to feature; MODIFIER	silent_mutation	Average:81.119; most accessible tissue: Minghui63 young leaf, score: 89.557	N	N	N	N
vg0507847236	A -> G	LOC_Os05g14034-LOC_Os05g14040	intergenic_region ; MODIFIER	silent_mutation	Average:81.119; most accessible tissue: Minghui63 young leaf, score: 89.557	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)
vg0507847236	A	G	0.0	0.01	0.0	0.0	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507847236	NA	3.36E-31	mr1039	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
vg0507847236	1.39E-06	1.92E-08	mr1039	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
vg0507847236	NA	7.73E-10	mr1514	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
vg0507847236	NA	2.41E-35	mr1632	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
vg0507847236	5.91E-06	2.01E-09	mr1632	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
vg0507847236	NA	4.93E-09	mr1986	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
vg0507847236	9.23E-10	6.17E-35	mr1039_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
vg0507847236	1.47E-09	5.86E-09	mr1039_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
vg0507847236	NA	1.08E-12	mr1514_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
vg0507847236	NA	2.05E-07	mr1607_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
vg0507847236	9.67E-11	2.75E-45	mr1632_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
vg0507847236	8.92E-10	1.16E-11	mr1632_2	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
vg0507847236	NA	9.33E-06	mr1720_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