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Detailed information for vg0123534663:

Variant ID: vg0123534663 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 23534663
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:

CAACTACTCTCCCGCTGATAGGGGGAACGGGGACGAGGAGGGCAACGAGGACAGGGGCTGGGTCCCGCCGCACGAGCTCCACCCCTGCATGAGCACGTCG[C/T]
TGCGTCCTTCGTGAGCGAGGGTAGCAGCAGCACACCCAAGGGAGGTTGGGACGAGGAGGGATGCATGAGCAGGGGATGGGTTTCGTCGTACAAGCTCCTT

Reverse complement sequence

AAGGAGCTTGTACGACGAAACCCATCCCCTGCTCATGCATCCCTCCTCGTCCCAACCTCCCTTGGGTGTGCTGCTGCTACCCTCGCTCACGAAGGACGCA[G/A]
CGACGTGCTCATGCAGGGGTGGAGCTCGTGCGGCGGGACCCAGCCCCTGTCCTCGTTGCCCTCCTCGTCCCCGTTCCCCCTATCAGCGGGAGAGTAGTTG

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	70.70%	29.10%	0.23%	0.00%	NA
All Indica	2759	60.70%	39.20%	0.11%	0.00%	NA
All Japonica	1512	98.60%	1.20%	0.20%	0.00%	NA
Aus	269	8.20%	91.80%	0.00%	0.00%	NA
Indica I	595	93.80%	6.20%	0.00%	0.00%	NA
Indica II	465	63.70%	36.10%	0.22%	0.00%	NA
Indica III	913	40.50%	59.50%	0.00%	0.00%	NA
Indica Intermediate	786	57.40%	42.40%	0.25%	0.00%	NA
Temperate Japonica	767	99.60%	0.30%	0.13%	0.00%	NA
Tropical Japonica	504	98.40%	1.60%	0.00%	0.00%	NA
Japonica Intermediate	241	95.90%	3.30%	0.83%	0.00%	NA
VI/Aromatic	96	88.50%	9.40%	2.08%	0.00%	NA
Intermediate	90	73.30%	23.30%	3.33%	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
vg0123534663	C -> T	LOC_Os01g41565.1	upstream_gene_variant ; 1932.0bp to feature; MODIFIER	silent_mutation	Average:82.33; most accessible tissue: Zhenshan97 panicle, score: 92.133	N	N	N	N
vg0123534663	C -> T	LOC_Os01g41565-LOC_Os01g41580	intergenic_region ; MODIFIER	silent_mutation	Average:82.33; most accessible tissue: Zhenshan97 panicle, score: 92.133	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)
vg0123534663	C	T	-0.02	-0.02	-0.02	-0.01	-0.02	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123534663	NA	7.43E-06	mr1346	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
vg0123534663	NA	6.11E-08	mr1561	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
vg0123534663	NA	4.15E-09	mr1587	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
vg0123534663	NA	3.27E-07	mr1908	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
vg0123534663	2.74E-06	2.73E-06	mr1996	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
vg0123534663	NA	5.09E-07	mr1380_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
vg0123534663	NA	4.26E-06	mr1522_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
vg0123534663	NA	9.32E-08	mr1561_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
vg0123534663	NA	4.17E-07	mr1908_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
vg0123534663	NA	4.18E-06	mr1996_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