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Detailed information for vg0128444492:

Variant ID: vg0128444492 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 28444492
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTCTCTTTAAAGCGCGCACACACACATATGGATGGATCAGCAGCTAGCTGCACAAGCAATAGCAATACATCGCCAGCGAGAACACGAGCTATCTGCATC[G/A]
ATGGCGGCGGCGCACTTTGTGTTCGTCCCGCTCATGGCGCAGGGCCACCTCATACCGGCGGTCGACACCGCACTGCTGCTGGCCACCCATGGCGTGCTCT

Reverse complement sequence

AGAGCACGCCATGGGTGGCCAGCAGCAGTGCGGTGTCGACCGCCGGTATGAGGTGGCCCTGCGCCATGAGCGGGACGAACACAAAGTGCGCCGCCGCCAT[C/T]
GATGCAGATAGCTCGTGTTCTCGCTGGCGATGTATTGCTATTGCTTGTGCAGCTAGCTGCTGATCCATCCATATGTGTGTGTGCGCGCTTTAAAGAGAGA

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	83.80%	16.10%	0.08%	0.00%	NA
All Indica	2759	76.60%	23.30%	0.11%	0.00%	NA
All Japonica	1512	95.20%	4.80%	0.00%	0.00%	NA
Aus	269	85.90%	14.10%	0.00%	0.00%	NA
Indica I	595	76.30%	23.50%	0.17%	0.00%	NA
Indica II	465	98.50%	1.50%	0.00%	0.00%	NA
Indica III	913	58.30%	41.70%	0.00%	0.00%	NA
Indica Intermediate	786	85.10%	14.60%	0.25%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	86.30%	13.70%	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	90.00%	8.90%	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
vg0128444492	G -> A	LOC_Os01g49450.1	upstream_gene_variant ; 2288.0bp to feature; MODIFIER	silent_mutation	Average:72.935; most accessible tissue: Zhenshan97 flag leaf, score: 93.147	N	N	N	N
vg0128444492	G -> A	LOC_Os01g49460.1	upstream_gene_variant ; 1.0bp to feature; MODIFIER	silent_mutation	Average:72.935; most accessible tissue: Zhenshan97 flag leaf, score: 93.147	N	N	N	N
vg0128444492	G -> A	LOC_Os01g49470.1	downstream_gene_variant ; 3395.0bp to feature; MODIFIER	silent_mutation	Average:72.935; most accessible tissue: Zhenshan97 flag leaf, score: 93.147	N	N	N	N
vg0128444492	G -> A	LOC_Os01g49470.2	downstream_gene_variant ; 3415.0bp to feature; MODIFIER	silent_mutation	Average:72.935; most accessible tissue: Zhenshan97 flag leaf, score: 93.147	N	N	N	N
vg0128444492	G -> A	LOC_Os01g49450-LOC_Os01g49460	intergenic_region ; MODIFIER	silent_mutation	Average:72.935; most accessible tissue: Zhenshan97 flag leaf, score: 93.147	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)
vg0128444492	G	A	-0.05	-0.04	-0.05	-0.03	-0.04	-0.06

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0128444492	NA	4.44E-06	mr1024_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
vg0128444492	NA	3.07E-06	mr1115_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
vg0128444492	NA	8.25E-06	mr1169_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
vg0128444492	NA	2.79E-06	mr1169_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
vg0128444492	NA	9.54E-07	mr1550_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
vg0128444492	NA	1.01E-06	mr1571_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
vg0128444492	4.23E-06	4.23E-06	mr1615_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
vg0128444492	NA	4.00E-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
vg0128444492	NA	7.09E-06	mr1735_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
vg0128444492	NA	3.81E-06	mr1735_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
vg0128444492	NA	1.64E-14	mr1739_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
vg0128444492	NA	2.31E-09	mr1739_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