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Detailed information for vg0202460448:

Variant ID: vg0202460448 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2460448
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGACGAGAATAGCGGAGCGCGAGAGAGAAGGGTGTTTACACCCAAATTTGGCACCTAGAGATAAAATAGGAAAAATTGCCAAAGTTTGGAAGTCTGCCG[G/A]
TTTTCTCCGAGTGGGCCGGTCTGACCACTGTGTGTTGAGCGGTCATACCGCCGGTTGAGGGCCGGTCAGACCGGCGGCATGTGGCCGGTCTGACCAGCAG

Reverse complement sequence

CTGCTGGTCAGACCGGCCACATGCCGCCGGTCTGACCGGCCCTCAACCGGCGGTATGACCGCTCAACACACAGTGGTCAGACCGGCCCACTCGGAGAAAA[C/T]
CGGCAGACTTCCAAACTTTGGCAATTTTTCCTATTTTATCTCTAGGTGCCAAATTTGGGTGTAAACACCCTTCTCTCTCGCGCTCCGCTATTCTCGTCCG

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	93.50%	2.60%	0.97%	2.92%	NA
All Indica	2759	97.80%	0.10%	0.22%	1.88%	NA
All Japonica	1512	89.50%	7.90%	2.25%	0.40%	NA
Aus	269	99.30%	0.00%	0.37%	0.37%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.10%	0.00%	0.00%	0.86%	NA
Indica III	913	96.90%	0.10%	0.00%	2.96%	NA
Indica Intermediate	786	96.60%	0.00%	0.76%	2.67%	NA
Temperate Japonica	767	87.60%	9.00%	3.39%	0.00%	NA
Tropical Japonica	504	93.50%	6.00%	0.60%	0.00%	NA
Japonica Intermediate	241	87.10%	8.30%	2.07%	2.49%	NA
VI/Aromatic	96	20.80%	0.00%	4.17%	75.00%	NA
Intermediate	90	87.80%	3.30%	1.11%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0202460448	G -> A	LOC_Os02g05140.1	upstream_gene_variant ; 300.0bp to feature; MODIFIER	silent_mutation	Average:74.961; most accessible tissue: Minghui63 flag leaf, score: 86.766	N	N	N	N
vg0202460448	G -> A	LOC_Os02g05150.1	upstream_gene_variant ; 647.0bp to feature; MODIFIER	silent_mutation	Average:74.961; most accessible tissue: Minghui63 flag leaf, score: 86.766	N	N	N	N
vg0202460448	G -> A	LOC_Os02g05160.1	upstream_gene_variant ; 4513.0bp to feature; MODIFIER	silent_mutation	Average:74.961; most accessible tissue: Minghui63 flag leaf, score: 86.766	N	N	N	N
vg0202460448	G -> A	LOC_Os02g05140-LOC_Os02g05150	intergenic_region ; MODIFIER	silent_mutation	Average:74.961; most accessible tissue: Minghui63 flag leaf, score: 86.766	N	N	N	N
vg0202460448	G -> DEL	N	N	silent_mutation	Average:74.961; most accessible tissue: Minghui63 flag leaf, score: 86.766	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)
vg0202460448	G	A	-0.02	-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
vg0202460448	NA	9.44E-07	mr1069	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
vg0202460448	6.33E-06	NA	mr1075	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
vg0202460448	NA	5.83E-06	mr1080	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
vg0202460448	5.87E-07	5.87E-07	mr1861	Jap_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