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Detailed information for vg0206270004:

Variant ID: vg0206270004 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 6270004
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.56, C: 0.44, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

GTAGTAGTAAATGCTTGACTTGGTTTTCTGTTTTCCTTCATTTTGCACCTTACTTCGATATGGCGTCTTCCTGCGTTATGGAGAACAATAGTACTACCCC[T/C]
AATCCCAAAATAAATGTAATTCTATGAGTCCACGGCGTGAAATTAATATGATATCGACGCTTGTTGAAAGTTGAAACCTTCCAAATTAAGCAATTAGTAC

Reverse complement sequence

GTACTAATTGCTTAATTTGGAAGGTTTCAACTTTCAACAAGCGTCGATATCATATTAATTTCACGCCGTGGACTCATAGAATTACATTTATTTTGGGATT[A/G]
GGGGTAGTACTATTGTTCTCCATAACGCAGGAAGACGCCATATCGAAGTAAGGTGCAAAATGAAGGAAAACAGAAAACCAAGTCAAGCATTTACTACTAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.50%	47.40%	0.15%	0.00%	NA
All Indica	2759	83.40%	16.40%	0.14%	0.00%	NA
All Japonica	1512	2.90%	97.00%	0.07%	0.00%	NA
Aus	269	29.00%	70.60%	0.37%	0.00%	NA
Indica I	595	99.20%	0.70%	0.17%	0.00%	NA
Indica II	465	65.20%	34.40%	0.43%	0.00%	NA
Indica III	913	82.00%	17.90%	0.11%	0.00%	NA
Indica Intermediate	786	84.00%	16.00%	0.00%	0.00%	NA
Temperate Japonica	767	2.30%	97.70%	0.00%	0.00%	NA
Tropical Japonica	504	3.40%	96.60%	0.00%	0.00%	NA
Japonica Intermediate	241	3.70%	95.90%	0.41%	0.00%	NA
VI/Aromatic	96	18.80%	80.20%	1.04%	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
vg0206270004	T -> C	LOC_Os02g12090.1	upstream_gene_variant ; 423.0bp to feature; MODIFIER	silent_mutation	Average:77.962; most accessible tissue: Zhenshan97 root, score: 95.515	N	N	N	N
vg0206270004	T -> C	LOC_Os02g12100.1	upstream_gene_variant ; 4682.0bp to feature; MODIFIER	silent_mutation	Average:77.962; most accessible tissue: Zhenshan97 root, score: 95.515	N	N	N	N
vg0206270004	T -> C	LOC_Os02g12070.1	downstream_gene_variant ; 3206.0bp to feature; MODIFIER	silent_mutation	Average:77.962; most accessible tissue: Zhenshan97 root, score: 95.515	N	N	N	N
vg0206270004	T -> C	LOC_Os02g12080.1	downstream_gene_variant ; 858.0bp to feature; MODIFIER	silent_mutation	Average:77.962; most accessible tissue: Zhenshan97 root, score: 95.515	N	N	N	N
vg0206270004	T -> C	LOC_Os02g12080-LOC_Os02g12090	intergenic_region ; MODIFIER	silent_mutation	Average:77.962; most accessible tissue: Zhenshan97 root, score: 95.515	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)
vg0206270004	T	C	0.03	0.0	0.0	0.0	0.01	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0206270004	NA	4.78E-09	mr1410	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
vg0206270004	NA	7.08E-14	mr1478	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
vg0206270004	NA	5.74E-16	mr1040_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
vg0206270004	1.49E-06	NA	mr1402_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
vg0206270004	NA	3.72E-07	mr1408_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
vg0206270004	NA	1.03E-07	mr1754_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
vg0206270004	NA	4.32E-06	mr1785_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
vg0206270004	NA	4.52E-08	mr1804_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
vg0206270004	NA	5.87E-07	mr1819_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
vg0206270004	NA	2.75E-06	mr1925_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
vg0206270004	NA	3.66E-22	mr1949_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