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Detailed information for vg0208281695:

Variant ID: vg0208281695 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8281695
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.72, A: 0.28, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

ACACAACCATTAAAAAACGCCAAAGGACGTGTGCCATATCATAAAAAATGTTCTCTAGAAGGGTGATTTTTAAAAAATGTCCTCTAGAAGAGTGATTTTT[T/A]
AAAAACACCCTCCCAAGGACGTTAGGGGTGTAGATTTGTAAAACTTTAATTAAAAATAGTTTTGTCAATATTTTACTAAATAAAATTAAAAATTAAAAAA

Reverse complement sequence

TTTTTTAATTTTTAATTTTATTTAGTAAAATATTGACAAAACTATTTTTAATTAAAGTTTTACAAATCTACACCCCTAACGTCCTTGGGAGGGTGTTTTT[A/T]
AAAAATCACTCTTCTAGAGGACATTTTTTAAAAATCACCCTTCTAGAGAACATTTTTTATGATATGGCACACGTCCTTTGGCGTTTTTTAATGGTTGTGT

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	53.30%	24.10%	0.25%	22.30%	NA
All Indica	2759	76.00%	1.20%	0.29%	22.47%	NA
All Japonica	1512	2.90%	71.20%	0.13%	25.73%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	59.30%	0.30%	0.67%	39.66%	NA
Indica II	465	91.20%	1.30%	0.00%	7.53%	NA
Indica III	913	80.50%	1.10%	0.11%	18.29%	NA
Indica Intermediate	786	74.40%	2.00%	0.38%	23.16%	NA
Temperate Japonica	767	1.70%	94.50%	0.00%	3.78%	NA
Tropical Japonica	504	4.20%	36.90%	0.40%	58.53%	NA
Japonica Intermediate	241	4.10%	68.90%	0.00%	26.97%	NA
VI/Aromatic	96	61.50%	5.20%	0.00%	33.33%	NA
Intermediate	90	56.70%	27.80%	2.22%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0208281695	T -> A	LOC_Os02g14874.1	downstream_gene_variant ; 3192.0bp to feature; MODIFIER	silent_mutation	Average:59.038; most accessible tissue: Minghui63 root, score: 89.361	N	N	N	N
vg0208281695	T -> A	LOC_Os02g14874.2	downstream_gene_variant ; 3282.0bp to feature; MODIFIER	silent_mutation	Average:59.038; most accessible tissue: Minghui63 root, score: 89.361	N	N	N	N
vg0208281695	T -> A	LOC_Os02g14874-LOC_Os02g14880	intergenic_region ; MODIFIER	silent_mutation	Average:59.038; most accessible tissue: Minghui63 root, score: 89.361	N	N	N	N
vg0208281695	T -> DEL	N	N	silent_mutation	Average:59.038; most accessible tissue: Minghui63 root, score: 89.361	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)
vg0208281695	T	A	-0.02	0.0	0.0	-0.01	0.0	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208281695	NA	6.73E-10	mr1232	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
vg0208281695	NA	6.10E-11	mr1336	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
vg0208281695	NA	2.22E-19	mr1557	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
vg0208281695	NA	1.23E-12	mr1579	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
vg0208281695	NA	6.08E-16	mr1636	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
vg0208281695	NA	7.73E-14	mr1641	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
vg0208281695	NA	7.05E-18	mr1909	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
vg0208281695	NA	3.32E-14	mr1921	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
vg0208281695	NA	3.25E-10	mr1232_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
vg0208281695	NA	1.70E-18	mr1557_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
vg0208281695	NA	1.23E-15	mr1767_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