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Detailed information for vg1219787869:

Variant ID: vg1219787869 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19787869
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.91, T: 0.09, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

TATCAATTTTCTCGTGTAAACTTCTAATCCTTTTCCCAGGAATTATCAAACAAGCCGTCGGAGTACTTGTTTGCGTCTTGTCAAATGCCGTGACAGGATA[A/T]
AACCAGGTATCGTGATCTTGTGACTGAAAGAACATTAGAGGGTTAGATTAGATTAAGACAACCTTGATTTGACACTTGGGGCCAAGCAGAGAAGAGAATT

Reverse complement sequence

AATTCTCTTCTCTGCTTGGCCCCAAGTGTCAAATCAAGGTTGTCTTAATCTAATCTAACCCTCTAATGTTCTTTCAGTCACAAGATCACGATACCTGGTT[T/A]
TATCCTGTCACGGCATTTGACAAGACGCAAACAAGTACTCCGACGGCTTGTTTGATAATTCCTGGGAAAAGGATTAGAAGTTTACACGAGAAAATTGATA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.40%	34.10%	0.23%	0.32%	NA
All Indica	2759	44.20%	54.90%	0.40%	0.54%	NA
All Japonica	1512	98.10%	1.90%	0.00%	0.00%	NA
Aus	269	82.50%	17.50%	0.00%	0.00%	NA
Indica I	595	64.00%	35.50%	0.34%	0.17%	NA
Indica II	465	9.00%	89.90%	0.43%	0.65%	NA
Indica III	913	52.10%	46.70%	0.33%	0.88%	NA
Indica Intermediate	786	40.70%	58.40%	0.51%	0.38%	NA
Temperate Japonica	767	98.80%	1.20%	0.00%	0.00%	NA
Tropical Japonica	504	96.80%	3.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	82.20%	17.80%	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
vg1219787869	A -> DEL	N	N	silent_mutation	Average:86.88; most accessible tissue: Minghui63 flag leaf, score: 96.689	N	N	N	N
vg1219787869	A -> T	LOC_Os12g32770.1	upstream_gene_variant ; 4163.0bp to feature; MODIFIER	silent_mutation	Average:86.88; most accessible tissue: Minghui63 flag leaf, score: 96.689	N	N	N	N
vg1219787869	A -> T	LOC_Os12g32750.1	downstream_gene_variant ; 1282.0bp to feature; MODIFIER	silent_mutation	Average:86.88; most accessible tissue: Minghui63 flag leaf, score: 96.689	N	N	N	N
vg1219787869	A -> T	LOC_Os12g32760.1	downstream_gene_variant ; 440.0bp to feature; MODIFIER	silent_mutation	Average:86.88; most accessible tissue: Minghui63 flag leaf, score: 96.689	N	N	N	N
vg1219787869	A -> T	LOC_Os12g32750-LOC_Os12g32760	intergenic_region ; MODIFIER	silent_mutation	Average:86.88; most accessible tissue: Minghui63 flag leaf, score: 96.689	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)
vg1219787869	A	T	0.02	-0.06	-0.05	0.0	-0.02	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219787869	2.48E-06	NA	mr1201	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
vg1219787869	NA	5.72E-08	mr1084_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
vg1219787869	NA	6.51E-08	mr1205_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
vg1219787869	NA	1.44E-08	mr1319_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
vg1219787869	NA	4.98E-07	mr1418_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
vg1219787869	NA	1.14E-06	mr1488_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
vg1219787869	NA	6.84E-06	mr1492_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
vg1219787869	NA	3.64E-12	mr1636_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
vg1219787869	NA	3.11E-09	mr1659_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
vg1219787869	NA	1.62E-07	mr1779_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
vg1219787869	NA	2.95E-08	mr1992_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