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Detailed information for vg0303252106:

Variant ID: vg0303252106 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 3252106
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCAAAATGCCATTTTGGACAAAAATGACCCTGGTTCTTCTCCCTTCCTCCAATACCAATGTCGGAGGAGCTCGTCGGCAGCCACCGGTGCCACCTTGTC[A/G]
GCGACGATGGGGGCGCTGCCCTCCTCGTCGTCCCCACCTTTTCATTATGCCCGCCGCGCTAAGAGGAGGCCATAGCCGACGTCATCAACGTTGATGGGGC

Reverse complement sequence

GCCCCATCAACGTTGATGACGTCGGCTATGGCCTCCTCTTAGCGCGGCGGGCATAATGAAAAGGTGGGGACGACGAGGAGGGCAGCGCCCCCATCGTCGC[T/C]
GACAAGGTGGCACCGGTGGCTGCCGACGAGCTCCTCCGACATTGGTATTGGAGGAAGGGAGAAGAACCAGGGTCATTTTTGTCCAAAATGGCATTTTGGT

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	58.70%	37.90%	1.52%	1.86%	NA
All Indica	2759	87.70%	7.20%	2.25%	2.90%	NA
All Japonica	1512	0.50%	99.50%	0.00%	0.00%	NA
Aus	269	97.80%	1.90%	0.37%	0.00%	NA
Indica I	595	95.80%	2.70%	1.34%	0.17%	NA
Indica II	465	88.60%	3.70%	2.15%	5.59%	NA
Indica III	913	89.40%	5.00%	2.19%	3.40%	NA
Indica Intermediate	786	79.00%	15.10%	3.05%	2.80%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	0.40%	99.60%	0.00%	0.00%	NA
Japonica Intermediate	241	0.80%	99.20%	0.00%	0.00%	NA
VI/Aromatic	96	42.70%	43.80%	6.25%	7.29%	NA
Intermediate	90	48.90%	46.70%	3.33%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0303252106	A -> DEL	N	N	silent_mutation	Average:81.722; most accessible tissue: Minghui63 panicle, score: 92.666	N	N	N	N
vg0303252106	A -> G	LOC_Os03g06490.1	upstream_gene_variant ; 881.0bp to feature; MODIFIER	silent_mutation	Average:81.722; most accessible tissue: Minghui63 panicle, score: 92.666	N	N	N	N
vg0303252106	A -> G	LOC_Os03g06480-LOC_Os03g06490	intergenic_region ; MODIFIER	silent_mutation	Average:81.722; most accessible tissue: Minghui63 panicle, score: 92.666	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)
vg0303252106	A	G	-0.04	-0.02	-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
vg0303252106	NA	1.95E-06	mr1015	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
vg0303252106	NA	6.41E-06	mr1181	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
vg0303252106	NA	2.44E-09	mr1191	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
vg0303252106	8.64E-07	8.64E-07	mr1449	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
vg0303252106	NA	5.33E-09	mr1644	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
vg0303252106	NA	5.83E-06	mr1981	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
vg0303252106	NA	2.73E-16	mr1114_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
vg0303252106	NA	1.19E-13	mr1191_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
vg0303252106	NA	1.33E-22	mr1242_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