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Detailed information for vg0306242443:

Variant ID: vg0306242443 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 6242443
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTACAGAATCTGTCAGTAAATCGCGAGATGAATTTATTAAGACTAATTAATCTGTCATTAATAAATGTTTACTGTAGCAACATATTGTCAAATTATGTG[G/A]
CAATTAGGCTTAAAAAATTTGTCTCGCAAATTAGTTGCAATCTGTGCAATTAGTTATTTTTAGCATATATTTAATACTTCATGTAGATGTTCAAACGTTC

Reverse complement sequence

GAACGTTTGAACATCTACATGAAGTATTAAATATATGCTAAAAATAACTAATTGCACAGATTGCAACTAATTTGCGAGACAAATTTTTTAAGCCTAATTG[C/T]
CACATAATTTGACAATATGTTGCTACAGTAAACATTTATTAATGACAGATTAATTAGTCTTAATAAATTCATCTCGCGATTTACTGACAGATTCTGTAAT

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	87.10%	3.20%	0.47%	9.25%	NA
All Indica	2759	83.90%	0.10%	0.29%	15.73%	NA
All Japonica	1512	89.30%	9.70%	0.86%	0.13%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	53.80%	0.00%	0.50%	45.71%	NA
Indica II	465	99.10%	0.20%	0.00%	0.65%	NA
Indica III	913	94.00%	0.00%	0.00%	6.02%	NA
Indica Intermediate	786	85.90%	0.30%	0.64%	13.23%	NA
Temperate Japonica	767	99.20%	0.10%	0.39%	0.26%	NA
Tropical Japonica	504	69.80%	28.40%	1.79%	0.00%	NA
Japonica Intermediate	241	98.30%	1.20%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	3.30%	1.11%	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
vg0306242443	G -> A	LOC_Os03g11900.1	upstream_gene_variant ; 4146.0bp to feature; MODIFIER	silent_mutation	Average:65.036; most accessible tissue: Zhenshan97 flag leaf, score: 95.246	N	N	N	N
vg0306242443	G -> A	LOC_Os03g11910.1	downstream_gene_variant ; 1547.0bp to feature; MODIFIER	silent_mutation	Average:65.036; most accessible tissue: Zhenshan97 flag leaf, score: 95.246	N	N	N	N
vg0306242443	G -> A	LOC_Os03g11910.2	downstream_gene_variant ; 1547.0bp to feature; MODIFIER	silent_mutation	Average:65.036; most accessible tissue: Zhenshan97 flag leaf, score: 95.246	N	N	N	N
vg0306242443	G -> A	LOC_Os03g11900-LOC_Os03g11910	intergenic_region ; MODIFIER	silent_mutation	Average:65.036; most accessible tissue: Zhenshan97 flag leaf, score: 95.246	N	N	N	N
vg0306242443	G -> DEL	N	N	silent_mutation	Average:65.036; most accessible tissue: Zhenshan97 flag leaf, score: 95.246	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)
vg0306242443	G	A	0.02	0.01	0.02	0.0	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0306242443	NA	1.41E-07	mr1042_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
vg0306242443	NA	3.31E-07	mr1047_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
vg0306242443	NA	9.98E-09	mr1742_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
vg0306242443	2.63E-07	2.40E-12	mr1798_2	Jap_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