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Detailed information for vg0524587903:

Variant ID: vg0524587903 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 24587903
Reference Allele: G	Alternative Allele: A,C
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

ACCGGAGCATGCGGGGCTACGACGCCATCAATCGGATCAAGGCGAGGCTGGAGACCGTCTGCCCGCTCACCGTCTCCTGCGCCGACATCATCGCCATGGC[G/A,C]
GCGAGAGACGCCGTCTACCTGGTACGCGCCTCACGGAACAAATCCATGGCTTCTTTGCAAATCGATATCGCGCTCTGCTTCTGAATGCTCCTTGATTCGC

Reverse complement sequence

GCGAATCAAGGAGCATTCAGAAGCAGAGCGCGATATCGATTTGCAAAGAAGCCATGGATTTGTTCCGTGAGGCGCGTACCAGGTAGACGGCGTCTCTCGC[C/T,G]
GCCATGGCGATGATGTCGGCGCAGGAGACGGTGAGCGGGCAGACGGTCTCCAGCCTCGCCTTGATCCGATTGATGGCGTCGTAGCCCCGCATGCTCCGGT

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	94.60%	5.40%	0.00%	0.00%	NA
All Indica	2759	99.00%	1.00%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	24.50%	75.50%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	99.20%	0.80%	0.00%	0.00%	NA
Indica Intermediate	786	97.70%	2.30%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	81.20%	18.80%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0524587903	G -> C	LOC_Os05g42000.1	synonymous_variant ; p.Ala137Ala; LOW	N	Average:84.071; most accessible tissue: Zhenshan97 flower, score: 94.106	N	N	N	N
vg0524587903	G -> C	LOC_Os05g41990.1	downstream_gene_variant ; 2958.0bp to feature; MODIFIER	N	Average:84.071; most accessible tissue: Zhenshan97 flower, score: 94.106	N	N	N	N
vg0524587903	G -> C	LOC_Os05g42010.1	downstream_gene_variant ; 421.0bp to feature; MODIFIER	N	Average:84.071; most accessible tissue: Zhenshan97 flower, score: 94.106	N	N	N	N
vg0524587903	G -> C	LOC_Os05g42010.2	downstream_gene_variant ; 421.0bp to feature; MODIFIER	N	Average:84.071; most accessible tissue: Zhenshan97 flower, score: 94.106	N	N	N	N
vg0524587903	G -> C	LOC_Os05g42000.2	intron_variant ; MODIFIER	N	Average:84.071; most accessible tissue: Zhenshan97 flower, score: 94.106	N	N	N	N
vg0524587903	G -> A	LOC_Os05g42000.1	synonymous_variant ; p.Ala137Ala; LOW	synonymous_codon	Average:84.071; most accessible tissue: Zhenshan97 flower, score: 94.106	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)
vg0524587903	G	A	0.03	0.01	-0.01	0.0	0.01	0.0
vg0524587903	G	C	0.02	0.0	0.0	0.0	0.02	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0524587903	NA	2.31E-08	mr1465	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
vg0524587903	NA	1.42E-10	mr1499	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
vg0524587903	8.07E-12	9.07E-22	mr1612	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
vg0524587903	NA	6.38E-07	mr1706	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
vg0524587903	NA	3.73E-09	mr1989	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
vg0524587903	NA	5.09E-10	mr1047_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
vg0524587903	4.59E-09	NA	mr1109_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
vg0524587903	NA	9.49E-08	mr1126_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
vg0524587903	NA	1.17E-09	mr1166_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
vg0524587903	8.54E-12	2.56E-18	mr1612_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
vg0524587903	NA	1.19E-06	mr1815_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