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Detailed information for vg0334419989:

Variant ID: vg0334419989 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 34419989
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGATTTTAAGACACAATATGTGTATAACAGGTGGGACCATATGTTAATAGTATAGTAATAGTATAGTAAGTAACTATTGTATGAATTGGCTATTAGATC[G/A]
GCTATAAATAAATTGGAGTTAGTAGTAGGCTATACTATTGAACTTGCTCTTAGCATACCAAAATCACCGGACTAACAACAGTGGACAGCAGTTGGTCGGT

Reverse complement sequence

ACCGACCAACTGCTGTCCACTGTTGTTAGTCCGGTGATTTTGGTATGCTAAGAGCAAGTTCAATAGTATAGCCTACTACTAACTCCAATTTATTTATAGC[C/T]
GATCTAATAGCCAATTCATACAATAGTTACTTACTATACTATTACTATACTATTAACATATGGTCCCACCTGTTATACACATATTGTGTCTTAAAATCCA

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	93.10%	4.40%	0.61%	1.84%	NA
All Indica	2759	88.80%	7.40%	1.05%	2.83%	NA
All Japonica	1512	99.90%	0.00%	0.00%	0.07%	NA
Aus	269	99.30%	0.00%	0.00%	0.74%	NA
Indica I	595	99.80%	0.00%	0.00%	0.17%	NA
Indica II	465	87.10%	11.00%	1.51%	0.43%	NA
Indica III	913	81.30%	11.80%	1.20%	5.70%	NA
Indica Intermediate	786	90.10%	5.60%	1.40%	2.93%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	90.00%	7.80%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0334419989	G -> A	LOC_Os03g60560.1	upstream_gene_variant ; 4191.0bp to feature; MODIFIER	silent_mutation	Average:93.751; most accessible tissue: Minghui63 flower, score: 98.207	N	N	N	N
vg0334419989	G -> A	LOC_Os03g60550.1	downstream_gene_variant ; 826.0bp to feature; MODIFIER	silent_mutation	Average:93.751; most accessible tissue: Minghui63 flower, score: 98.207	N	N	N	N
vg0334419989	G -> A	LOC_Os03g60550.2	downstream_gene_variant ; 826.0bp to feature; MODIFIER	silent_mutation	Average:93.751; most accessible tissue: Minghui63 flower, score: 98.207	N	N	N	N
vg0334419989	G -> A	LOC_Os03g60550.3	downstream_gene_variant ; 826.0bp to feature; MODIFIER	silent_mutation	Average:93.751; most accessible tissue: Minghui63 flower, score: 98.207	N	N	N	N
vg0334419989	G -> A	LOC_Os03g60550-LOC_Os03g60560	intergenic_region ; MODIFIER	silent_mutation	Average:93.751; most accessible tissue: Minghui63 flower, score: 98.207	N	N	N	N
vg0334419989	G -> DEL	N	N	silent_mutation	Average:93.751; most accessible tissue: Minghui63 flower, score: 98.207	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)
vg0334419989	G	A	0.01	0.01	0.01	0.0	0.0	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0334419989	NA	4.11E-06	mr1113_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
vg0334419989	NA	9.29E-06	mr1114_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
vg0334419989	NA	2.40E-06	mr1117_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
vg0334419989	NA	1.64E-06	mr1119_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
vg0334419989	NA	1.36E-06	mr1120_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
vg0334419989	1.94E-06	2.44E-06	mr1240_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
vg0334419989	NA	6.37E-06	mr1247_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