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Detailed information for vg0518471877:

Variant ID: vg0518471877 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 18471877
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

CGCCGCCTCCTCCTTTGCCTGCATCGTGCCAGCACCACCCCTAATCCGGTACCACCACCAAGCTCCATCCGCCGCAAGCTAGCTTCTTGCCACCCACCTC[G/A]
CCGTCTGAGGCCGTCACTGGGGGAGGAGAAGGGAGAGGGGAGAGGCGACACCGCCTAGCTTGTGGGTGCACTGGCGTGGGGCAGAGAGAGGGAGGAGGGA

Reverse complement sequence

TCCCTCCTCCCTCTCTCTGCCCCACGCCAGTGCACCCACAAGCTAGGCGGTGTCGCCTCTCCCCTCTCCCTTCTCCTCCCCCAGTGACGGCCTCAGACGG[C/T]
GAGGTGGGTGGCAAGAAGCTAGCTTGCGGCGGATGGAGCTTGGTGGTGGTACCGGATTAGGGGTGGTGCTGGCACGATGCAGGCAAAGGAGGAGGCGGCG

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	77.70%	22.30%	0.04%	0.00%	NA
All Indica	2759	65.60%	34.30%	0.07%	0.00%	NA
All Japonica	1512	97.80%	2.20%	0.00%	0.00%	NA
Aus	269	77.70%	22.30%	0.00%	0.00%	NA
Indica I	595	54.60%	45.20%	0.17%	0.00%	NA
Indica II	465	92.50%	7.50%	0.00%	0.00%	NA
Indica III	913	66.70%	33.20%	0.11%	0.00%	NA
Indica Intermediate	786	56.90%	43.10%	0.00%	0.00%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	95.20%	4.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	14.40%	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
vg0518471877	G -> A	LOC_Os05g31720.1	downstream_gene_variant ; 1228.0bp to feature; MODIFIER	silent_mutation	Average:79.832; most accessible tissue: Zhenshan97 young leaf, score: 90.638	N	N	N	N
vg0518471877	G -> A	LOC_Os05g31730.1	downstream_gene_variant ; 3646.0bp to feature; MODIFIER	silent_mutation	Average:79.832; most accessible tissue: Zhenshan97 young leaf, score: 90.638	N	N	N	N
vg0518471877	G -> A	LOC_Os05g31720-LOC_Os05g31730	intergenic_region ; MODIFIER	silent_mutation	Average:79.832; most accessible tissue: Zhenshan97 young leaf, score: 90.638	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)
vg0518471877	G	A	0.01	0.01	0.01	0.01	0.01	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0518471877	NA	3.21E-06	mr1029	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
vg0518471877	NA	4.48E-09	mr1189	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
vg0518471877	NA	3.02E-06	mr1189	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
vg0518471877	NA	1.59E-08	mr1625	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
vg0518471877	NA	2.61E-06	mr1625	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
vg0518471877	NA	1.92E-06	mr1684	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
vg0518471877	NA	7.52E-07	mr1734	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
vg0518471877	NA	4.49E-07	mr1796	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
vg0518471877	NA	1.97E-08	mr1860	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
vg0518471877	NA	9.30E-06	mr1860	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
vg0518471877	NA	1.35E-07	mr1990	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
vg0518471877	NA	2.14E-07	mr1458_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