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Detailed information for vg0431851987:

Variant ID: vg0431851987 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 31851987
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTCGCCAGAGCGCCACTACCGCCGCCGCCGCCGATGCCTTGCTCCCCTGCTCCCGTGTCGTCGCCGGCCACCGGACCTCCTCTCCCGCCTCGCCCCATC[G/A]
GTCTCCTCCCTACCTGGTGGTCGGCCTGCCCAGAGCCCAAGAGAGAAGAGTGAGAGAGAGAGAGAGAGGAGGAAGGGAGAGAAGAGGGGAAAGAGAGAGA

Reverse complement sequence

TCTCTCTCTTTCCCCTCTTCTCTCCCTTCCTCCTCTCTCTCTCTCTCTCACTCTTCTCTCTTGGGCTCTGGGCAGGCCGACCACCAGGTAGGGAGGAGAC[C/T]
GATGGGGCGAGGCGGGAGAGGAGGTCCGGTGGCCGGCGACGACACGGGAGCAGGGGAGCAAGGCATCGGCGGCGGCGGCGGTAGTGGCGCTCTGGCGAGC

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	80.90%	18.80%	0.28%	0.00%	NA
All Indica	2759	93.90%	5.80%	0.29%	0.00%	NA
All Japonica	1512	62.90%	36.90%	0.20%	0.00%	NA
Aus	269	62.80%	36.40%	0.74%	0.00%	NA
Indica I	595	98.50%	1.50%	0.00%	0.00%	NA
Indica II	465	95.50%	4.50%	0.00%	0.00%	NA
Indica III	913	91.10%	8.80%	0.11%	0.00%	NA
Indica Intermediate	786	92.90%	6.20%	0.89%	0.00%	NA
Temperate Japonica	767	89.40%	10.30%	0.26%	0.00%	NA
Tropical Japonica	504	33.70%	66.10%	0.20%	0.00%	NA
Japonica Intermediate	241	39.40%	60.60%	0.00%	0.00%	NA
VI/Aromatic	96	40.60%	59.40%	0.00%	0.00%	NA
Intermediate	90	80.00%	20.00%	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
vg0431851987	G -> A	LOC_Os04g53490.1	upstream_gene_variant ; 1119.0bp to feature; MODIFIER	silent_mutation	Average:75.364; most accessible tissue: Minghui63 panicle, score: 86.85	N	N	N	N
vg0431851987	G -> A	LOC_Os04g53496.1	upstream_gene_variant ; 2442.0bp to feature; MODIFIER	silent_mutation	Average:75.364; most accessible tissue: Minghui63 panicle, score: 86.85	N	N	N	N
vg0431851987	G -> A	LOC_Os04g53490-LOC_Os04g53496	intergenic_region ; MODIFIER	silent_mutation	Average:75.364; most accessible tissue: Minghui63 panicle, score: 86.85	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)
vg0431851987	G	A	-0.02	-0.02	-0.01	-0.01	-0.01	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0431851987	NA	2.14E-10	Heading_date	All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0431851987	NA	1.37E-07	mr1249	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
vg0431851987	NA	7.18E-06	mr1531	Jap_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
vg0431851987	NA	1.96E-06	mr1590	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
vg0431851987	NA	3.09E-06	mr1051_2	Jap_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
vg0431851987	NA	3.67E-07	mr1229_2	Jap_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
vg0431851987	NA	7.24E-08	mr1880_2	Jap_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