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Detailed information for vg0139807295:

Variant ID: vg0139807295 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 39807295
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAAAACAAACCTAAAACTAGATACTATCATATATTCTAGTGCAACAAATTATAGACATACTTCTACTAGTATATATCACGTTCAGTTTTAGATTTTTTT[T/A]
AAAAAACATATGTAGAGTAGTCGAATGCAAGATTGCAATGCAGGGATCAGGTCACCAGGACAACGGATGGGCCATGCACCCATCGCCGTCGCCGGCCGCG

Reverse complement sequence

CGCGGCCGGCGACGGCGATGGGTGCATGGCCCATCCGTTGTCCTGGTGACCTGATCCCTGCATTGCAATCTTGCATTCGACTACTCTACATATGTTTTTT[A/T]
AAAAAAATCTAAAACTGAACGTGATATATACTAGTAGAAGTATGTCTATAATTTGTTGCACTAGAATATATGATAGTATCTAGTTTTAGGTTTGTTTTTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.80%	11.10%	0.06%	0.00%	NA
All Indica	2759	88.70%	11.20%	0.11%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	50.20%	49.80%	0.00%	0.00%	NA
Indica I	595	93.30%	6.70%	0.00%	0.00%	NA
Indica II	465	98.50%	1.50%	0.00%	0.00%	NA
Indica III	913	82.90%	17.10%	0.00%	0.00%	NA
Indica Intermediate	786	86.30%	13.40%	0.38%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.50%	0.00%	0.00%	NA
VI/Aromatic	96	30.20%	69.80%	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
vg0139807295	T -> A	LOC_Os01g68500.1	upstream_gene_variant ; 4778.0bp to feature; MODIFIER	silent_mutation	Average:91.3; most accessible tissue: Zhenshan97 panicle, score: 96.414	N	N	N	N
vg0139807295	T -> A	LOC_Os01g68510.1	upstream_gene_variant ; 3008.0bp to feature; MODIFIER	silent_mutation	Average:91.3; most accessible tissue: Zhenshan97 panicle, score: 96.414	N	N	N	N
vg0139807295	T -> A	LOC_Os01g68524.1	downstream_gene_variant ; 4427.0bp to feature; MODIFIER	silent_mutation	Average:91.3; most accessible tissue: Zhenshan97 panicle, score: 96.414	N	N	N	N
vg0139807295	T -> A	LOC_Os01g68524.2	downstream_gene_variant ; 4427.0bp to feature; MODIFIER	silent_mutation	Average:91.3; most accessible tissue: Zhenshan97 panicle, score: 96.414	N	N	N	N
vg0139807295	T -> A	LOC_Os01g68500-LOC_Os01g68510	intergenic_region ; MODIFIER	silent_mutation	Average:91.3; most accessible tissue: Zhenshan97 panicle, score: 96.414	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)
vg0139807295	T	A	0.03	-0.03	-0.02	0.0	-0.01	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0139807295	NA	2.39E-06	mr1094	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
vg0139807295	NA	4.88E-07	mr1111	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
vg0139807295	NA	7.59E-07	mr1144	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
vg0139807295	NA	4.67E-06	mr1798	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
vg0139807295	NA	2.75E-07	mr1094_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
vg0139807295	NA	6.37E-08	mr1096_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
vg0139807295	NA	1.49E-07	mr1111_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
vg0139807295	NA	1.78E-07	mr1121_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
vg0139807295	1.66E-06	NA	mr1123_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
vg0139807295	NA	1.42E-08	mr1144_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
vg0139807295	1.17E-07	NA	mr1242_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
vg0139807295	NA	4.19E-10	mr1798_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