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Detailed information for vg1200249590:

Variant ID: vg1200249590 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 249590
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGATGGGGGGTTATTAAGGAAAAAGAGGCCATATGTTTGTTGCAAAGCAATAGAGAAGCCAAGCAGGCAGCCACTAAATTGGGTTGGGGTGCCTCCTCCT[C/T]
CCTTTCTTTCTTTCATCTGCTTCGTCCTCAGATCCGATCTCTCTTCTCTTGTTCTGGGGTTGGGGTCTCACGACCCGCCGCCTTCTTCGTCCCCGTCGCT

Reverse complement sequence

AGCGACGGGGACGAAGAAGGCGGCGGGTCGTGAGACCCCAACCCCAGAACAAGAGAAGAGAGATCGGATCTGAGGACGAAGCAGATGAAAGAAAGAAAGG[G/A]
AGGAGGAGGCACCCCAACCCAATTTAGTGGCTGCCTGCTTGGCTTCTCTATTGCTTTGCAACAAACATATGGCCTCTTTTTCCTTAATAACCCCCCATCA

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	57.50%	41.80%	0.04%	0.66%	NA
All Indica	2759	89.30%	9.60%	0.00%	1.05%	NA
All Japonica	1512	4.20%	95.80%	0.00%	0.00%	NA
Aus	269	55.80%	43.50%	0.00%	0.74%	NA
Indica I	595	95.80%	3.90%	0.00%	0.34%	NA
Indica II	465	93.80%	5.80%	0.00%	0.43%	NA
Indica III	913	82.80%	15.40%	0.00%	1.75%	NA
Indica Intermediate	786	89.30%	9.50%	0.00%	1.15%	NA
Temperate Japonica	767	6.00%	94.00%	0.00%	0.00%	NA
Tropical Japonica	504	2.60%	97.40%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	6.20%	93.80%	0.00%	0.00%	NA
Intermediate	90	35.60%	62.20%	2.22%	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
vg1200249590	C -> DEL	N	N	silent_mutation	Average:95.79; most accessible tissue: Zhenshan97 flower, score: 98.043	N	N	N	N
vg1200249590	C -> T	LOC_Os12g01390.1	upstream_gene_variant ; 135.0bp to feature; MODIFIER	silent_mutation	Average:95.79; most accessible tissue: Zhenshan97 flower, score: 98.043	N	N	N	N
vg1200249590	C -> T	LOC_Os12g01380.1	downstream_gene_variant ; 2201.0bp to feature; MODIFIER	silent_mutation	Average:95.79; most accessible tissue: Zhenshan97 flower, score: 98.043	N	N	N	N
vg1200249590	C -> T	LOC_Os12g01380-LOC_Os12g01390	intergenic_region ; MODIFIER	silent_mutation	Average:95.79; most accessible tissue: Zhenshan97 flower, score: 98.043	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)
vg1200249590	C	T	-0.03	-0.03	-0.02	-0.01	0.0	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200249590	NA	3.37E-15	mr1164	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
vg1200249590	NA	1.31E-06	mr1850	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
vg1200249590	NA	4.89E-20	mr1362_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
vg1200249590	3.72E-07	NA	mr1410_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