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Detailed information for vg1207276357:

Variant ID: vg1207276357 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7276357
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

ACATTTGCTAATGACGGATTAATTAGGCTTAATAAATTCGTCTCGCAGTTTACTGATGGATTCTGTAATTAGTTTTTTTATTAGTGCTCGAACACCCCAT[G/A]
CGACACCCTATATAATACTTTATGTGACACGCCAAAACTTTACACCCGTGGATCTAAACACCCCCTATATATGCATTAATGCAAACCAAATTGATCAGAG

Reverse complement sequence

CTCTGATCAATTTGGTTTGCATTAATGCATATATAGGGGGTGTTTAGATCCACGGGTGTAAAGTTTTGGCGTGTCACATAAAGTATTATATAGGGTGTCG[C/T]
ATGGGGTGTTCGAGCACTAATAAAAAAACTAATTACAGAATCCATCAGTAAACTGCGAGACGAATTTATTAAGCCTAATTAATCCGTCATTAGCAAATGT

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	87.10%	11.30%	0.57%	1.04%	NA
All Indica	2759	86.50%	11.10%	0.87%	1.59%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	34.20%	63.20%	0.74%	1.86%	NA
Indica I	595	88.60%	9.10%	2.18%	0.17%	NA
Indica II	465	90.50%	8.80%	0.22%	0.43%	NA
Indica III	913	86.70%	10.20%	0.66%	2.41%	NA
Indica Intermediate	786	82.20%	14.90%	0.51%	2.42%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	43.80%	56.20%	0.00%	0.00%	NA
Intermediate	90	93.30%	5.60%	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
vg1207276357	G -> DEL	N	N	silent_mutation	Average:66.142; most accessible tissue: Minghui63 panicle, score: 90.184	N	N	N	N
vg1207276357	G -> A	LOC_Os12g13090.1	upstream_gene_variant ; 406.0bp to feature; MODIFIER	silent_mutation	Average:66.142; most accessible tissue: Minghui63 panicle, score: 90.184	N	N	N	N
vg1207276357	G -> A	LOC_Os12g13080-LOC_Os12g13090	intergenic_region ; MODIFIER	silent_mutation	Average:66.142; most accessible tissue: Minghui63 panicle, score: 90.184	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)
vg1207276357	G	A	0.0	0.0	-0.01	0.01	0.0	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207276357	2.34E-06	9.51E-06	mr1062	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
vg1207276357	1.80E-06	6.76E-07	mr1261	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
vg1207276357	2.57E-06	9.30E-07	mr1324	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
vg1207276357	7.11E-06	2.70E-06	mr1335	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
vg1207276357	3.11E-06	3.11E-06	mr1429	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
vg1207276357	2.00E-06	NA	mr1482	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
vg1207276357	NA	4.93E-06	mr1522	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
vg1207276357	NA	7.60E-06	mr1553	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
vg1207276357	2.09E-06	1.11E-06	mr1660	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
vg1207276357	NA	7.21E-06	mr1705	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
vg1207276357	NA	9.98E-06	mr1772	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
vg1207276357	NA	7.51E-07	mr1815	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