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Detailed information for vg0104202598:

Variant ID: vg0104202598 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 4202598
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, C: 0.02, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

GCGGCGCGCACATGCAGATGCACACGCGTTGCAGAAGTGCAGAGGAGTACTGGTGCCATGGGCCTACGTGTACATGACGCAGCTAGCACTAGCTCGTGGC[A/C]
CTGGGAAATTCACTTTATACACTCCAACACTCCCTCTTACACGAGACCCTATTAAATCTCAAGCGTGCTTCCTCTCACACGAGATCCTATCAAATCTCAA

Reverse complement sequence

TTGAGATTTGATAGGATCTCGTGTGAGAGGAAGCACGCTTGAGATTTAATAGGGTCTCGTGTAAGAGGGAGTGTTGGAGTGTATAAAGTGAATTTCCCAG[T/G]
GCCACGAGCTAGTGCTAGCTGCGTCATGTACACGTAGGCCCATGGCACCAGTACTCCTCTGCACTTCTGCAACGCGTGTGCATCTGCATGTGCGCGCCGC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.30%	22.30%	7.36%	22.05%	NA
All Indica	2759	20.40%	34.70%	10.44%	34.47%	NA
All Japonica	1512	87.80%	4.40%	3.44%	4.43%	NA
Aus	269	92.60%	1.90%	1.49%	4.09%	NA
Indica I	595	26.60%	28.20%	9.24%	35.97%	NA
Indica II	465	4.70%	46.70%	13.12%	35.48%	NA
Indica III	913	23.70%	32.60%	9.97%	33.73%	NA
Indica Intermediate	786	21.20%	34.90%	10.31%	33.59%	NA
Temperate Japonica	767	96.90%	0.90%	0.65%	1.56%	NA
Tropical Japonica	504	70.20%	10.70%	8.93%	10.12%	NA
Japonica Intermediate	241	95.40%	2.10%	0.83%	1.66%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	58.90%	22.20%	4.44%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0104202598	A -> DEL	N	N	silent_mutation	Average:98.131; most accessible tissue: Zhenshan97 panicle, score: 99.254	N	N	N	N
vg0104202598	A -> C	LOC_Os01g08500.1	upstream_gene_variant ; 1282.0bp to feature; MODIFIER	silent_mutation	Average:98.131; most accessible tissue: Zhenshan97 panicle, score: 99.254	N	N	N	N
vg0104202598	A -> C	LOC_Os01g08490.1	downstream_gene_variant ; 3765.0bp to feature; MODIFIER	silent_mutation	Average:98.131; most accessible tissue: Zhenshan97 panicle, score: 99.254	N	N	N	N
vg0104202598	A -> C	LOC_Os01g08500-LOC_Os01g08510	intergenic_region ; MODIFIER	silent_mutation	Average:98.131; most accessible tissue: Zhenshan97 panicle, score: 99.254	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)
vg0104202598	A	C	0.03	0.18	0.17	0.01	0.01	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0104202598	NA	1.25E-11	mr1180	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
vg0104202598	NA	5.10E-14	mr1183	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
vg0104202598	5.97E-07	NA	mr1263	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
vg0104202598	NA	2.62E-09	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
vg0104202598	NA	6.33E-09	mr1352	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
vg0104202598	5.97E-07	NA	mr1451	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
vg0104202598	NA	7.30E-14	mr1503	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
vg0104202598	NA	6.18E-07	mr1622	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
vg0104202598	NA	5.27E-06	mr1653	Jap_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
vg0104202598	NA	2.41E-17	mr1180_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
vg0104202598	NA	3.53E-20	mr1183_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
vg0104202598	NA	1.39E-06	mr1418_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
vg0104202598	NA	1.46E-06	mr1498_2	Jap_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
vg0104202598	NA	6.97E-07	mr1834_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