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Detailed information for vg0619014811:

Variant ID: vg0619014811 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19014811
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGTCAACCTAAGGGACCACGGTGGACCGGGTACACAGAGACGGTCCGCGGGTCGACGAAAGCGGACCCCGTGTATCAACTGAGGCGAGTAGCCGACAAA[C/T]
GGACTCCACCAGACACCACGCGGGCTGCACACGTGGAAACCACGTGGCTACCGAGCGGGCACACTAACACGGTCTCCACACGCACAAGCGAACGACTACC

Reverse complement sequence

GGTAGTCGTTCGCTTGTGCGTGTGGAGACCGTGTTAGTGTGCCCGCTCGGTAGCCACGTGGTTTCCACGTGTGCAGCCCGCGTGGTGTCTGGTGGAGTCC[G/A]
TTTGTCGGCTACTCGCCTCAGTTGATACACGGGGTCCGCTTTCGTCGACCCGCGGACCGTCTCTGTGTACCCGGTCCACCGTGGTCCCTTAGGTTGACAT

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	94.20%	5.70%	0.02%	0.11%	NA
All Indica	2759	91.20%	8.70%	0.04%	0.00%	NA
All Japonica	1512	99.20%	0.50%	0.00%	0.33%	NA
Aus	269	93.30%	6.70%	0.00%	0.00%	NA
Indica I	595	87.70%	12.30%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	87.50%	12.40%	0.11%	0.00%	NA
Indica Intermediate	786	93.50%	6.50%	0.00%	0.00%	NA
Temperate Japonica	767	99.20%	0.10%	0.00%	0.65%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0619014811	C -> T	LOC_Os06g32700.1	upstream_gene_variant ; 471.0bp to feature; MODIFIER	silent_mutation	Average:76.435; most accessible tissue: Minghui63 flag leaf, score: 95.052	N	N	N	N
vg0619014811	C -> T	LOC_Os06g32690.1	downstream_gene_variant ; 3281.0bp to feature; MODIFIER	silent_mutation	Average:76.435; most accessible tissue: Minghui63 flag leaf, score: 95.052	N	N	N	N
vg0619014811	C -> T	LOC_Os06g32710.1	downstream_gene_variant ; 2223.0bp to feature; MODIFIER	silent_mutation	Average:76.435; most accessible tissue: Minghui63 flag leaf, score: 95.052	N	N	N	N
vg0619014811	C -> T	LOC_Os06g32690-LOC_Os06g32700	intergenic_region ; MODIFIER	silent_mutation	Average:76.435; most accessible tissue: Minghui63 flag leaf, score: 95.052	N	N	N	N
vg0619014811	C -> DEL	N	N	silent_mutation	Average:76.435; most accessible tissue: Minghui63 flag leaf, score: 95.052	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)
vg0619014811	C	T	-0.01	-0.01	-0.02	-0.01	-0.01	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619014811	NA	5.19E-07	mr1043_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
vg0619014811	NA	7.26E-06	mr1098_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
vg0619014811	NA	8.61E-06	mr1223_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
vg0619014811	NA	6.15E-06	mr1277_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
vg0619014811	NA	9.16E-08	mr1291_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
vg0619014811	NA	3.09E-07	mr1502_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
vg0619014811	NA	1.38E-07	mr1543_2	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
vg0619014811	NA	1.40E-06	mr1677_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
vg0619014811	NA	1.93E-06	mr1860_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
vg0619014811	NA	8.05E-07	mr1904_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
vg0619014811	9.73E-06	9.72E-06	mr1912_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