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Detailed information for vg0614838575:

Variant ID: vg0614838575 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 14838575
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGCCCAACAACAGCGGCATAATAGGCCAGCCGTGCAGGCGGAAACACCAGTCAGCGGCGGACGCTGTGGCCGATCGGTGAAGACGTAGACGCCCAGTAAC[G/A]
ACGGCATAATAGGCCAGTCGTGCAGACGAGGACACCAGTCGGCGGCAACGACGGCAAGCCGGTTGGTGAAGATGTGGACGCCCATCAACGGCGACATAAT

Reverse complement sequence

ATTATGTCGCCGTTGATGGGCGTCCACATCTTCACCAACCGGCTTGCCGTCGTTGCCGCCGACTGGTGTCCTCGTCTGCACGACTGGCCTATTATGCCGT[C/T]
GTTACTGGGCGTCTACGTCTTCACCGATCGGCCACAGCGTCCGCCGCTGACTGGTGTTTCCGCCTGCACGGCTGGCCTATTATGCCGCTGTTGTTGGGCG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.40%	6.80%	0.80%	0.00%	NA
All Indica	2759	99.00%	0.70%	0.25%	0.00%	NA
All Japonica	1512	86.10%	13.10%	0.79%	0.00%	NA
Aus	269	59.10%	34.60%	6.32%	0.00%	NA
Indica I	595	99.70%	0.00%	0.34%	0.00%	NA
Indica II	465	98.90%	0.90%	0.22%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	97.60%	1.90%	0.51%	0.00%	NA
Temperate Japonica	767	98.30%	1.40%	0.26%	0.00%	NA
Tropical Japonica	504	63.30%	35.30%	1.39%	0.00%	NA
Japonica Intermediate	241	95.00%	3.70%	1.24%	0.00%	NA
VI/Aromatic	96	96.90%	2.10%	1.04%	0.00%	NA
Intermediate	90	88.90%	10.00%	1.11%	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
vg0614838575	G -> A	LOC_Os06g25320.1	upstream_gene_variant ; 4282.0bp to feature; MODIFIER	silent_mutation	Average:62.2; most accessible tissue: Zhenshan97 flag leaf, score: 87.472	N	N	N	N
vg0614838575	G -> A	LOC_Os06g25330.1	downstream_gene_variant ; 289.0bp to feature; MODIFIER	silent_mutation	Average:62.2; most accessible tissue: Zhenshan97 flag leaf, score: 87.472	N	N	N	N
vg0614838575	G -> A	LOC_Os06g25340.1	downstream_gene_variant ; 3352.0bp to feature; MODIFIER	silent_mutation	Average:62.2; most accessible tissue: Zhenshan97 flag leaf, score: 87.472	N	N	N	N
vg0614838575	G -> A	LOC_Os06g25330-LOC_Os06g25340	intergenic_region ; MODIFIER	silent_mutation	Average:62.2; most accessible tissue: Zhenshan97 flag leaf, score: 87.472	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)
vg0614838575	G	A	-0.01	-0.01	-0.01	-0.01	-0.01	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0614838575	NA	3.42E-06	mr1248	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
vg0614838575	NA	6.80E-10	mr1379	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
vg0614838575	NA	3.53E-06	mr1382	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
vg0614838575	NA	1.07E-08	mr1559	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
vg0614838575	NA	1.99E-07	mr1236_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
vg0614838575	2.38E-06	2.75E-08	mr1252_2	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
vg0614838575	NA	1.19E-08	mr1263_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
vg0614838575	NA	6.24E-06	mr1295_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
vg0614838575	NA	4.33E-07	mr1363_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
vg0614838575	NA	7.48E-06	mr1419_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
vg0614838575	NA	3.05E-06	mr1420_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
vg0614838575	NA	2.80E-06	mr1736_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
vg0614838575	NA	2.41E-08	mr1805_2	Jap_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