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Detailed information for vg1219662792:

Variant ID: vg1219662792 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19662792
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGGGCCTGTTCACTTTGATGCCAAAAAAAAAATCTTACCAAATTTTGGCAATTGGCATGATTTCTTATATAGCTACTAAAATTTGACAGCAAACTAAAT[G/A]
TAGCTACTTTTCTGACAATTTTACCGAAATTTGATAAGGTTGAAAATGATATCGAAATAAACAAAACAGACTCTAAACTCAGCCGGGATGTCGTTTTGTC

Reverse complement sequence

GACAAAACGACATCCCGGCTGAGTTTAGAGTCTGTTTTGTTTATTTCGATATCATTTTCAACCTTATCAAATTTCGGTAAAATTGTCAGAAAAGTAGCTA[C/T]
ATTTAGTTTGCTGTCAAATTTTAGTAGCTATATAAGAAATCATGCCAATTGCCAAAATTTGGTAAGATTTTTTTTTTGGCATCAAAGTGAACAGGCCCTT

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	94.30%	5.50%	0.19%	0.00%	NA
All Indica	2759	94.70%	5.10%	0.18%	0.00%	NA
All Japonica	1512	99.20%	0.70%	0.07%	0.00%	NA
Aus	269	60.20%	38.70%	1.12%	0.00%	NA
Indica I	595	98.50%	1.30%	0.17%	0.00%	NA
Indica II	465	82.80%	17.20%	0.00%	0.00%	NA
Indica III	913	98.10%	1.90%	0.00%	0.00%	NA
Indica Intermediate	786	94.90%	4.60%	0.51%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	96.30%	3.70%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg1219662792	G -> A	LOC_Os12g32580.1	upstream_gene_variant ; 2270.0bp to feature; MODIFIER	silent_mutation	Average:91.944; most accessible tissue: Minghui63 root, score: 96.839	N	N	N	N
vg1219662792	G -> A	LOC_Os12g32590.1	upstream_gene_variant ; 315.0bp to feature; MODIFIER	silent_mutation	Average:91.944; most accessible tissue: Minghui63 root, score: 96.839	N	N	N	N
vg1219662792	G -> A	LOC_Os12g32580-LOC_Os12g32590	intergenic_region ; MODIFIER	silent_mutation	Average:91.944; most accessible tissue: Minghui63 root, score: 96.839	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)
vg1219662792	G	A	0.05	0.04	0.02	0.02	0.02	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219662792	2.45E-06	8.14E-08	mr1268	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
vg1219662792	NA	8.13E-06	mr1729_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
vg1219662792	NA	8.15E-06	mr1736_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
vg1219662792	NA	9.14E-07	mr1915_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
vg1219662792	2.62E-06	2.62E-06	mr1972_2	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