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Detailed information for vg1222486091:

Variant ID: vg1222486091 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22486091
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGCCGGACCACCTCCTCCTCGCCTAGCCGTCGCCGGCCCTCCCCCCCCCCCCCCCCGAACCGCCGCCGCCGCCGGACCTTCTCCTCCTCACCCAGCCGAG[C/T]
CGACCTCGCGCGCTGGCTCTCCTTGCAGGCTCCGAGGAGAGGGAGGGGGAGAGAGAGAGAGGGGAGGGGAGGATAAGGTTTGAGTGGTGGCCTGGTGGGG

Reverse complement sequence

CCCCACCAGGCCACCACTCAAACCTTATCCTCCCCTCCCCTCTCTCTCTCTCCCCCTCCCTCTCCTCGGAGCCTGCAAGGAGAGCCAGCGCGCGAGGTCG[G/A]
CTCGGCTGGGTGAGGAGGAGAAGGTCCGGCGGCGGCGGCGGTTCGGGGGGGGGGGGGGGGAGGGCCGGCGACGGCTAGGCGAGGAGGAGGTGGTCCGGCG

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	76.40%	5.20%	1.10%	17.33%	NA
All Indica	2759	70.80%	8.80%	1.70%	18.70%	NA
All Japonica	1512	90.50%	0.10%	0.20%	9.13%	NA
Aus	269	41.60%	0.00%	0.74%	57.62%	NA
Indica I	595	86.20%	0.70%	2.02%	11.09%	NA
Indica II	465	77.60%	0.60%	0.65%	21.08%	NA
Indica III	913	56.20%	17.90%	1.42%	24.53%	NA
Indica Intermediate	786	72.00%	9.30%	2.42%	16.28%	NA
Temperate Japonica	767	96.70%	0.30%	0.26%	2.74%	NA
Tropical Japonica	504	78.40%	0.00%	0.20%	21.43%	NA
Japonica Intermediate	241	96.30%	0.00%	0.00%	3.73%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	90.00%	0.00%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222486091	C -> DEL	N	N	silent_mutation	Average:81.624; most accessible tissue: Zhenshan97 young leaf, score: 95.133	N	N	N	N
vg1222486091	C -> T	LOC_Os12g36690.1	upstream_gene_variant ; 4804.0bp to feature; MODIFIER	silent_mutation	Average:81.624; most accessible tissue: Zhenshan97 young leaf, score: 95.133	N	N	N	N
vg1222486091	C -> T	LOC_Os12g36700.1	upstream_gene_variant ; 3268.0bp to feature; MODIFIER	silent_mutation	Average:81.624; most accessible tissue: Zhenshan97 young leaf, score: 95.133	N	N	N	N
vg1222486091	C -> T	LOC_Os12g36710.1	upstream_gene_variant ; 1487.0bp to feature; MODIFIER	silent_mutation	Average:81.624; most accessible tissue: Zhenshan97 young leaf, score: 95.133	N	N	N	N
vg1222486091	C -> T	LOC_Os12g36720.1	downstream_gene_variant ; 1246.0bp to feature; MODIFIER	silent_mutation	Average:81.624; most accessible tissue: Zhenshan97 young leaf, score: 95.133	N	N	N	N
vg1222486091	C -> T	LOC_Os12g36710-LOC_Os12g36720	intergenic_region ; MODIFIER	silent_mutation	Average:81.624; most accessible tissue: Zhenshan97 young leaf, score: 95.133	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)
vg1222486091	C	T	0.07	0.04	0.04	0.01	0.03	0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222486091	NA	3.85E-06	mr1060_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
vg1222486091	NA	8.31E-06	mr1060_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
vg1222486091	NA	7.43E-07	mr1358_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
vg1222486091	NA	1.74E-06	mr1378_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
vg1222486091	6.59E-06	3.36E-10	mr1446_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
vg1222486091	3.58E-06	5.04E-09	mr1446_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
vg1222486091	NA	9.57E-07	mr1624_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
vg1222486091	NA	7.77E-06	mr1946_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
vg1222486091	NA	7.77E-06	mr1948_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