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Detailed information for vg0727791557:

Variant ID: vg0727791557 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 27791557
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.67, T: 0.33, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

GCTTATAAACATTATGATTCAACAAATATATCGGCGTTAGATAGAGTTTCTGGTGGGACAAGCGCCAGGGAGACCAGTTGCTTCAGAACTCCAAGATCTC[A/T]
AGGCGAGATCTTCCCAGAGAGGAGTTGTTGCCACCTGGTCCATATTACAGTTCGGCATCACCTAACTGGTCTGCAAAGTTTGTAAGCAAATGCATTTCTT

Reverse complement sequence

AAGAAATGCATTTGCTTACAAACTTTGCAGACCAGTTAGGTGATGCCGAACTGTAATATGGACCAGGTGGCAACAACTCCTCTCTGGGAAGATCTCGCCT[T/A]
GAGATCTTGGAGTTCTGAAGCAACTGGTCTCCCTGGCGCTTGTCCCACCAGAAACTCTATCTAACGCCGATATATTTGTTGAATCATAATGTTTATAAGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.20%	44.60%	0.19%	0.00%	NA
All Indica	2759	88.90%	10.80%	0.29%	0.00%	NA
All Japonica	1512	4.70%	95.20%	0.07%	0.00%	NA
Aus	269	0.70%	99.30%	0.00%	0.00%	NA
Indica I	595	95.00%	4.00%	1.01%	0.00%	NA
Indica II	465	90.80%	9.00%	0.22%	0.00%	NA
Indica III	913	89.80%	10.20%	0.00%	0.00%	NA
Indica Intermediate	786	82.20%	17.70%	0.13%	0.00%	NA
Temperate Japonica	767	1.00%	99.00%	0.00%	0.00%	NA
Tropical Japonica	504	11.50%	88.30%	0.20%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	49.00%	51.00%	0.00%	0.00%	NA
Intermediate	90	42.20%	57.80%	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
vg0727791557	A -> T	LOC_Os07g46540.1	3_prime_UTR_variant ; 58.0bp to feature; MODIFIER	silent_mutation	Average:78.299; most accessible tissue: Minghui63 flag leaf, score: 97.494	N	N	N	N
vg0727791557	A -> T	LOC_Os07g46520.1	upstream_gene_variant ; 4637.0bp to feature; MODIFIER	silent_mutation	Average:78.299; most accessible tissue: Minghui63 flag leaf, score: 97.494	N	N	N	N
vg0727791557	A -> T	LOC_Os07g46530.1	downstream_gene_variant ; 580.0bp to feature; MODIFIER	silent_mutation	Average:78.299; most accessible tissue: Minghui63 flag leaf, score: 97.494	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)
vg0727791557	A	T	-0.03	0.01	-0.01	0.01	0.0	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0727791557	NA	5.13E-35	mr1094	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
vg0727791557	NA	2.79E-37	mr1110	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
vg0727791557	NA	6.19E-32	mr1208	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
vg0727791557	NA	4.55E-18	mr1255	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
vg0727791557	NA	5.63E-10	mr1260	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
vg0727791557	1.14E-06	1.14E-06	mr1260	Ind_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
vg0727791557	NA	2.25E-09	mr1299	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
vg0727791557	NA	3.75E-07	mr1716	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
vg0727791557	NA	4.54E-35	mr1828	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
vg0727791557	NA	2.17E-18	mr1913	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
vg0727791557	NA	3.70E-10	mr1927	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
vg0727791557	NA	1.33E-38	mr1110_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
vg0727791557	NA	4.93E-20	mr1218_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
vg0727791557	NA	6.29E-18	mr1870_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