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Detailed information for vg1122219057:

Variant ID: vg1122219057 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22219057
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.75, A: 0.24, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

AAAAAACCATGTCTGTATTCCCTACCAATCTGAAATATAAAAGATCAAATTTGTGCGCAATCAACTACAAGTTGCTCCATTTTTTTTCTCATATTCTCTG[A/G]
TGATATACACACATCATTTTCCTGTGCGCAATTCTTGAAATTCAGAGTTTTGATATTTCTGCATATACTCCTTGAAAGTTTTCTTATGCGCAATTCTTGA

Reverse complement sequence

TCAAGAATTGCGCATAAGAAAACTTTCAAGGAGTATATGCAGAAATATCAAAACTCTGAATTTCAAGAATTGCGCACAGGAAAATGATGTGTGTATATCA[T/C]
CAGAGAATATGAGAAAAAAAATGGAGCAACTTGTAGTTGATTGCGCACAAATTTGATCTTTTATATTTCAGATTGGTAGGGAATACAGACATGGTTTTTT

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	60.30%	29.30%	5.69%	4.63%	NA
All Indica	2759	68.00%	17.20%	8.30%	6.52%	NA
All Japonica	1512	39.90%	58.10%	0.79%	1.12%	NA
Aus	269	85.10%	0.70%	8.18%	5.95%	NA
Indica I	595	47.90%	35.30%	13.78%	3.03%	NA
Indica II	465	74.60%	2.20%	14.19%	9.03%	NA
Indica III	913	74.70%	16.10%	1.53%	7.67%	NA
Indica Intermediate	786	71.50%	13.60%	8.52%	6.36%	NA
Temperate Japonica	767	31.00%	66.50%	1.17%	1.30%	NA
Tropical Japonica	504	52.20%	46.40%	0.20%	1.19%	NA
Japonica Intermediate	241	42.70%	56.00%	0.83%	0.41%	NA
VI/Aromatic	96	89.60%	6.20%	0.00%	4.17%	NA
Intermediate	90	63.30%	27.80%	6.67%	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
vg1122219057	A -> DEL	N	N	silent_mutation	Average:71.448; most accessible tissue: Zhenshan97 flower, score: 88.928	N	N	N	N
vg1122219057	A -> G	LOC_Os11g37640.1	3_prime_UTR_variant ; 209.0bp to feature; MODIFIER	silent_mutation	Average:71.448; most accessible tissue: Zhenshan97 flower, score: 88.928	N	N	N	N
vg1122219057	A -> G	LOC_Os11g37660.1	downstream_gene_variant ; 4594.0bp to feature; MODIFIER	silent_mutation	Average:71.448; most accessible tissue: Zhenshan97 flower, score: 88.928	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)
vg1122219057	A	G	0.01	0.01	0.01	0.0	0.01	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122219057	2.83E-06	NA	mr1081	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
vg1122219057	NA	2.31E-08	mr1252	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
vg1122219057	NA	6.02E-06	mr1502	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
vg1122219057	NA	6.21E-06	mr1965	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