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Detailed information for vg0606864427:

Variant ID: vg0606864427 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 6864427
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCGTGCGTGGAGCTTAGTTGTCTACCGTATTAGAGCAGGTACAATAGCCGGCTATAACCATATATCGAGAAGAAAAAAGAAGAGAGAGAAGAAAGCGGG[C/T]
TACAGATTTGTAGCCGGCTGCAACACAGACTTCAAGATATTTTGTGTGTATGAGAGGTGGGATCGGATATTAAGAGCAAGTTTAATAGTATAGCCAACTA

Reverse complement sequence

TAGTTGGCTATACTATTAAACTTGCTCTTAATATCCGATCCCACCTCTCATACACACAAAATATCTTGAAGTCTGTGTTGCAGCCGGCTACAAATCTGTA[G/A]
CCCGCTTTCTTCTCTCTCTTCTTTTTTCTTCTCGATATATGGTTATAGCCGGCTATTGTACCTGCTCTAATACGGTAGACAACTAAGCTCCACGCACGCA

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	85.10%	14.70%	0.21%	0.00%	NA
All Indica	2759	75.00%	24.60%	0.36%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	96.30%	2.40%	1.34%	0.00%	NA
Indica II	465	72.70%	27.30%	0.00%	0.00%	NA
Indica III	913	56.30%	43.60%	0.11%	0.00%	NA
Indica Intermediate	786	82.10%	17.80%	0.13%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0606864427	C -> T	LOC_Os06g12610.1	upstream_gene_variant ; 1966.0bp to feature; MODIFIER	silent_mutation	Average:74.207; most accessible tissue: Zhenshan97 panicle, score: 93.02	N	N	N	N
vg0606864427	C -> T	LOC_Os06g12600-LOC_Os06g12610	intergenic_region ; MODIFIER	silent_mutation	Average:74.207; most accessible tissue: Zhenshan97 panicle, score: 93.02	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)
vg0606864427	C	T	0.02	-0.01	0.01	0.02	0.02	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0606864427	NA	3.10E-06	mr1064	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
vg0606864427	NA	3.22E-06	mr1221	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
vg0606864427	NA	3.09E-06	mr1352	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
vg0606864427	2.18E-06	6.44E-09	mr1377	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
vg0606864427	3.83E-07	3.83E-07	mr1377	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
vg0606864427	NA	6.73E-06	mr1531	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
vg0606864427	NA	7.57E-08	mr1534	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
vg0606864427	NA	2.26E-06	mr1691	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
vg0606864427	NA	2.90E-06	mr1870	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
vg0606864427	NA	5.34E-06	mr1881	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
vg0606864427	NA	3.41E-07	mr1951	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