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Detailed information for vg0432594893:

Variant ID: vg0432594893 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32594893
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, T: 0.21, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

ATTCTTGTTTTTTCTTTCGTCGCAGTGGTTTTGCCGGTTTGAGCATAGTAAAACGTGCGTTACTTTCACCGTGCTTTTCCATATGAAAATGTGTACCCAT[T/C]
GTAAAAAGTACTTCTAAGCTAGCTACAGTAGATTCTAGGGGAGAAATTTACTATGGTTATTGTTACGGCGCTTCTTTTAACCTGGAAGTAGCTTGGCAAC

Reverse complement sequence

GTTGCCAAGCTACTTCCAGGTTAAAAGAAGCGCCGTAACAATAACCATAGTAAATTTCTCCCCTAGAATCTACTGTAGCTAGCTTAGAAGTACTTTTTAC[A/G]
ATGGGTACACATTTTCATATGGAAAAGCACGGTGAAAGTAACGCACGTTTTACTATGCTCAAACCGGCAAAACCACTGCGACGAAAGAAAAAACAAGAAT

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	67.40%	32.00%	0.34%	0.28%	NA
All Indica	2759	75.30%	24.00%	0.33%	0.40%	NA
All Japonica	1512	63.40%	36.40%	0.20%	0.07%	NA
Aus	269	12.30%	87.40%	0.00%	0.37%	NA
Indica I	595	89.60%	9.70%	0.50%	0.17%	NA
Indica II	465	81.50%	18.10%	0.00%	0.43%	NA
Indica III	913	59.10%	40.00%	0.44%	0.44%	NA
Indica Intermediate	786	79.60%	19.60%	0.25%	0.51%	NA
Temperate Japonica	767	70.90%	28.80%	0.26%	0.00%	NA
Tropical Japonica	504	67.50%	32.30%	0.00%	0.20%	NA
Japonica Intermediate	241	30.70%	68.90%	0.41%	0.00%	NA
VI/Aromatic	96	61.50%	38.50%	0.00%	0.00%	NA
Intermediate	90	63.30%	32.20%	4.44%	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
vg0432594893	T -> C	LOC_Os04g54810.1	intron_variant ; MODIFIER	silent_mutation	Average:75.117; most accessible tissue: Zhenshan97 panicle, score: 93.244	N	N	N	N
vg0432594893	T -> DEL	N	N	silent_mutation	Average:75.117; most accessible tissue: Zhenshan97 panicle, score: 93.244	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)
vg0432594893	T	C	0.01	0.04	0.04	0.02	0.04	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432594893	NA	1.00E-08	mr1403	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
vg0432594893	NA	5.89E-08	mr1403	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
vg0432594893	2.54E-06	1.17E-08	mr1800	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
vg0432594893	1.80E-06	3.87E-08	mr1800	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
vg0432594893	NA	2.66E-06	mr1544_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
vg0432594893	NA	8.16E-07	mr1740_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
vg0432594893	1.86E-07	4.01E-09	mr1741_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
vg0432594893	3.01E-07	NA	mr1784_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
vg0432594893	NA	8.68E-06	mr1786_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
vg0432594893	9.25E-11	NA	mr1800_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
vg0432594893	6.96E-11	2.35E-12	mr1800_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
vg0432594893	9.67E-06	NA	mr1873_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