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Detailed information for vg1003461178:

Variant ID: vg1003461178 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3461178
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.73, C: 0.28, others allele: 0.00, population size: 51. )

Flanking Sequence (100 bp) in Reference Genome:

AGCCCAAACCTGTAATCTGCCTGAGACGTGTTTGGTTGCTATCCTGAGAATTTTAGCCTGAGGATTCTTGCCTGACGAAACTTGCCTGAGTCAGGCGTAG[T/C]
AAAAAGGTCGCCTGAGCAAGCCATGGCATTTCCACCAACATGCCTGAGTAGAATCACCTCTCTTCTACCACTACTTCTCCTCACTGTACCACCGTAGGGT

Reverse complement sequence

ACCCTACGGTGGTACAGTGAGGAGAAGTAGTGGTAGAAGAGAGGTGATTCTACTCAGGCATGTTGGTGGAAATGCCATGGCTTGCTCAGGCGACCTTTTT[A/G]
CTACGCCTGACTCAGGCAAGTTTCGTCAGGCAAGAATCCTCAGGCTAAAATTCTCAGGATAGCAACCAAACACGTCTCAGGCAGATTACAGGTTTGGGCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.40%	0.10%	2.98%	50.53%	NA
All Indica	2759	22.40%	0.20%	3.01%	74.37%	NA
All Japonica	1512	97.90%	0.00%	0.13%	1.92%	NA
Aus	269	5.20%	0.40%	7.81%	86.62%	NA
Indica I	595	25.00%	0.30%	1.34%	73.28%	NA
Indica II	465	16.10%	0.20%	0.43%	83.23%	NA
Indica III	913	26.10%	0.10%	6.46%	67.36%	NA
Indica Intermediate	786	20.00%	0.10%	1.78%	78.12%	NA
Temperate Japonica	767	99.20%	0.00%	0.13%	0.65%	NA
Tropical Japonica	504	96.00%	0.00%	0.00%	3.97%	NA
Japonica Intermediate	241	97.90%	0.00%	0.41%	1.66%	NA
VI/Aromatic	96	35.40%	0.00%	32.29%	32.29%	NA
Intermediate	90	47.80%	0.00%	4.44%	47.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1003461178	T -> C	LOC_Os10g06680.1	upstream_gene_variant ; 1650.0bp to feature; MODIFIER	silent_mutation	Average:65.861; most accessible tissue: Zhenshan97 panicle, score: 95.016	N	N	N	N
vg1003461178	T -> C	LOC_Os10g06660.1	downstream_gene_variant ; 3557.0bp to feature; MODIFIER	silent_mutation	Average:65.861; most accessible tissue: Zhenshan97 panicle, score: 95.016	N	N	N	N
vg1003461178	T -> C	LOC_Os10g06670.1	downstream_gene_variant ; 781.0bp to feature; MODIFIER	silent_mutation	Average:65.861; most accessible tissue: Zhenshan97 panicle, score: 95.016	N	N	N	N
vg1003461178	T -> C	LOC_Os10g06690.1	downstream_gene_variant ; 3221.0bp to feature; MODIFIER	silent_mutation	Average:65.861; most accessible tissue: Zhenshan97 panicle, score: 95.016	N	N	N	N
vg1003461178	T -> C	LOC_Os10g06670-LOC_Os10g06680	intergenic_region ; MODIFIER	silent_mutation	Average:65.861; most accessible tissue: Zhenshan97 panicle, score: 95.016	N	N	N	N
vg1003461178	T -> DEL	N	N	silent_mutation	Average:65.861; most accessible tissue: Zhenshan97 panicle, score: 95.016	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)
vg1003461178	T	C	-0.02	-0.02	-0.01	-0.01	0.0	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003461178	NA	7.39E-06	mr1538	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
vg1003461178	3.12E-06	3.05E-07	mr1547	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
vg1003461178	NA	3.48E-06	mr1646	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
vg1003461178	2.23E-10	NA	mr1709	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
vg1003461178	2.30E-10	3.73E-11	mr1709	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
vg1003461178	NA	2.29E-07	mr1779	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
vg1003461178	NA	9.49E-08	mr1538_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
vg1003461178	2.04E-06	NA	mr1547_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
vg1003461178	1.30E-07	6.90E-10	mr1547_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
vg1003461178	8.27E-15	NA	mr1709_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
vg1003461178	6.75E-14	1.03E-11	mr1709_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