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Detailed information for vg0314557350:

Variant ID: vg0314557350 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14557350
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, A: 0.29, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

AAATGAAGAGATGCACACATGTCTCGGCCTCAACAGAGCCCATATTTGATACATTACCTTCTCTCTCTTTTTTTTAAGAAACGACAGTAGGAGTTCTACC[A/G]
GAATTTAATTGACCCTGTTTATAAGGAAAACCAGATCAAAAACCATACAACTGCACAGTTTTGCTACAGGGAACCCGGCGAAACCCCACAGAAGACAAAG

Reverse complement sequence

CTTTGTCTTCTGTGGGGTTTCGCCGGGTTCCCTGTAGCAAAACTGTGCAGTTGTATGGTTTTTGATCTGGTTTTCCTTATAAACAGGGTCAATTAAATTC[T/C]
GGTAGAACTCCTACTGTCGTTTCTTAAAAAAAAGAGAGAGAAGGTAATGTATCAAATATGGGCTCTGTTGAGGCCGAGACATGTGTGCATCTCTTCATTT

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	67.50%	31.80%	0.17%	0.49%	NA
All Indica	2759	53.00%	46.00%	0.18%	0.80%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	29.40%	69.90%	0.74%	0.00%	NA
Indica I	595	49.20%	50.10%	0.34%	0.34%	NA
Indica II	465	20.40%	78.50%	0.00%	1.08%	NA
Indica III	913	76.70%	22.70%	0.11%	0.55%	NA
Indica Intermediate	786	47.70%	50.80%	0.25%	1.27%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	91.70%	7.30%	1.04%	0.00%	NA
Intermediate	90	63.30%	35.60%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0314557350	A -> DEL	N	N	silent_mutation	Average:77.976; most accessible tissue: Zhenshan97 flower, score: 98.37	N	N	N	N
vg0314557350	A -> G	LOC_Os03g25490.1	upstream_gene_variant ; 1972.0bp to feature; MODIFIER	silent_mutation	Average:77.976; most accessible tissue: Zhenshan97 flower, score: 98.37	N	N	N	N
vg0314557350	A -> G	LOC_Os03g25490.2	upstream_gene_variant ; 1972.0bp to feature; MODIFIER	silent_mutation	Average:77.976; most accessible tissue: Zhenshan97 flower, score: 98.37	N	N	N	N
vg0314557350	A -> G	LOC_Os03g25470.1	downstream_gene_variant ; 4601.0bp to feature; MODIFIER	silent_mutation	Average:77.976; most accessible tissue: Zhenshan97 flower, score: 98.37	N	N	N	N
vg0314557350	A -> G	LOC_Os03g25480.1	downstream_gene_variant ; 1121.0bp to feature; MODIFIER	silent_mutation	Average:77.976; most accessible tissue: Zhenshan97 flower, score: 98.37	N	N	N	N
vg0314557350	A -> G	LOC_Os03g25480-LOC_Os03g25490	intergenic_region ; MODIFIER	silent_mutation	Average:77.976; most accessible tissue: Zhenshan97 flower, score: 98.37	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)
vg0314557350	A	G	0.01	0.03	0.02	0.02	0.0	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314557350	1.75E-73	8.00E-162	mr1542	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
vg0314557350	2.64E-56	1.48E-95	mr1542	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
vg0314557350	NA	4.79E-07	mr1587	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
vg0314557350	NA	2.57E-08	mr1644	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
vg0314557350	NA	2.93E-08	mr1902	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
vg0314557350	7.24E-07	5.06E-20	mr1281_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
vg0314557350	1.22E-06	1.22E-06	mr1281_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
vg0314557350	1.54E-80	1.24E-187	mr1542_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
vg0314557350	1.21E-76	3.70E-115	mr1542_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
vg0314557350	1.64E-18	4.01E-31	mr1587_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
vg0314557350	2.52E-14	3.32E-16	mr1587_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