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Detailed information for vg0614933791:

Variant ID: vg0614933791 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 14933791
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTCGTCCCAATAAACTGAAAAGGCCCACATGTCATCCAAATAAAGGAAGCTTCCTGCAGTACTCAAACAGTTAATACATTGCCCCACGATGACCACTAA[C/T]
CATGCATGCACTCAGCAAATAACTGAAAGGGCCCACATGTCATCCAAATAAAGGAAGCTTCCTGTAGTAATCAGTTAGTTAACCCATTGTCTCACGATTA

Reverse complement sequence

TAATCGTGAGACAATGGGTTAACTAACTGATTACTACAGGAAGCTTCCTTTATTTGGATGACATGTGGGCCCTTTCAGTTATTTGCTGAGTGCATGCATG[G/A]
TTAGTGGTCATCGTGGGGCAATGTATTAACTGTTTGAGTACTGCAGGAAGCTTCCTTTATTTGGATGACATGTGGGCCTTTTCAGTTTATTGGGACGAAC

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	61.90%	37.90%	0.17%	0.00%	NA
All Indica	2759	96.20%	3.50%	0.29%	0.00%	NA
All Japonica	1512	9.00%	91.00%	0.00%	0.00%	NA
Aus	269	29.70%	70.30%	0.00%	0.00%	NA
Indica I	595	94.80%	4.40%	0.84%	0.00%	NA
Indica II	465	98.50%	1.30%	0.22%	0.00%	NA
Indica III	913	98.10%	1.90%	0.00%	0.00%	NA
Indica Intermediate	786	93.80%	6.00%	0.25%	0.00%	NA
Temperate Japonica	767	3.80%	96.20%	0.00%	0.00%	NA
Tropical Japonica	504	17.70%	82.30%	0.00%	0.00%	NA
Japonica Intermediate	241	7.50%	92.50%	0.00%	0.00%	NA
VI/Aromatic	96	12.50%	87.50%	0.00%	0.00%	NA
Intermediate	90	48.90%	51.10%	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
vg0614933791	C -> T	LOC_Os06g25540.1	upstream_gene_variant ; 190.0bp to feature; MODIFIER	silent_mutation	Average:78.643; most accessible tissue: Zhenshan97 flower, score: 91.609	N	N	N	N
vg0614933791	C -> T	LOC_Os06g25550.1	upstream_gene_variant ; 3601.0bp to feature; MODIFIER	silent_mutation	Average:78.643; most accessible tissue: Zhenshan97 flower, score: 91.609	N	N	N	N
vg0614933791	C -> T	LOC_Os06g25530.1	downstream_gene_variant ; 1485.0bp to feature; MODIFIER	silent_mutation	Average:78.643; most accessible tissue: Zhenshan97 flower, score: 91.609	N	N	N	N
vg0614933791	C -> T	LOC_Os06g25530-LOC_Os06g25540	intergenic_region ; MODIFIER	silent_mutation	Average:78.643; most accessible tissue: Zhenshan97 flower, score: 91.609	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)
vg0614933791	C	T	0.03	0.02	0.01	-0.03	0.04	0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0614933791	NA	2.80E-06	mr1020	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
vg0614933791	3.22E-07	3.22E-07	mr1032	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
vg0614933791	1.88E-06	1.19E-06	mr1071	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
vg0614933791	9.24E-06	1.82E-06	mr1080	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
vg0614933791	6.55E-07	1.04E-06	mr1203	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
vg0614933791	NA	4.50E-06	mr1395	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
vg0614933791	1.17E-07	1.17E-07	mr1478	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
vg0614933791	6.39E-06	5.22E-06	mr1618	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
vg0614933791	NA	4.50E-07	mr1716	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
vg0614933791	NA	1.28E-07	mr1971	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
vg0614933791	NA	6.20E-16	mr1033_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
vg0614933791	NA	4.94E-09	mr1536_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