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Detailed information for vg0224289132:

Variant ID: vg0224289132 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24289132
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

ATAAATTAGGATCCTTGTTATGAGAGTAAAATCATTAGCAGCTGACATCAGAGAGTCGGCATAGCAGAGAGTGACATAAATTAGGCACCAAACCAACACA[C/T]
GATAAATGCAGTTTATGAAATTCAATAAATCCGTAACATGAGCCGTGACTTACCGATGATGGTGCAGGTCACAACGGTCGCAGAGTCGTAGTCGTCGTAG

Reverse complement sequence

CTACGACGACTACGACTCTGCGACCGTTGTGACCTGCACCATCATCGGTAAGTCACGGCTCATGTTACGGATTTATTGAATTTCATAAACTGCATTTATC[G/A]
TGTGTTGGTTTGGTGCCTAATTTATGTCACTCTCTGCTATGCCGACTCTCTGATGTCAGCTGCTAATGATTTTACTCTCATAACAAGGATCCTAATTTAT

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	90.20%	9.10%	0.72%	0.00%	NA
All Indica	2759	92.90%	7.00%	0.04%	0.00%	NA
All Japonica	1512	85.30%	12.50%	2.18%	0.00%	NA
Aus	269	89.60%	10.40%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	82.80%	17.00%	0.22%	0.00%	NA
Indica III	913	95.90%	4.10%	0.00%	0.00%	NA
Indica Intermediate	786	90.30%	9.70%	0.00%	0.00%	NA
Temperate Japonica	767	83.60%	13.30%	3.13%	0.00%	NA
Tropical Japonica	504	91.70%	7.30%	0.99%	0.00%	NA
Japonica Intermediate	241	77.60%	20.70%	1.66%	0.00%	NA
VI/Aromatic	96	88.50%	11.50%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0224289132	C -> T	LOC_Os02g40110.1	upstream_gene_variant ; 4328.0bp to feature; MODIFIER	silent_mutation	Average:80.191; most accessible tissue: Zhenshan97 flower, score: 89.362	N	N	N	N
vg0224289132	C -> T	LOC_Os02g40130.1	upstream_gene_variant ; 4003.0bp to feature; MODIFIER	silent_mutation	Average:80.191; most accessible tissue: Zhenshan97 flower, score: 89.362	N	N	N	N
vg0224289132	C -> T	LOC_Os02g40120.1	intron_variant ; MODIFIER	silent_mutation	Average:80.191; most accessible tissue: Zhenshan97 flower, score: 89.362	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)
vg0224289132	C	T	-0.04	-0.03	-0.05	-0.03	-0.04	-0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224289132	4.04E-06	2.51E-06	mr1034	Jap_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
vg0224289132	NA	1.01E-06	mr1069	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
vg0224289132	NA	9.15E-08	mr1149	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
vg0224289132	NA	7.31E-07	mr1667	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
vg0224289132	NA	4.99E-06	mr1868	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
vg0224289132	4.71E-06	3.48E-11	mr1072_2	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
vg0224289132	NA	4.99E-10	mr1075_2	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
vg0224289132	NA	3.32E-10	mr1077_2	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
vg0224289132	NA	4.54E-08	mr1124_2	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
vg0224289132	NA	3.44E-10	mr1149_2	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
vg0224289132	NA	5.76E-06	mr1406_2	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
vg0224289132	NA	1.11E-09	mr1441_2	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
vg0224289132	NA	1.85E-07	mr1592_2	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
vg0224289132	8.98E-06	5.53E-09	mr1861_2	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