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Detailed information for vg1221121568:

Variant ID: vg1221121568 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21121568
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.58, A: 0.42, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

AATTCCTGGCTATGAATATGGATATGTGCATATGTCCATATTCATAGCCAGGAATTGGTTCTTATTGGGACGGAGGGAGTACGCTGCGCTGAGCATGGCA[G/A]
CTTGCCGAGGAGACATTCACACGGTGGGGATGATAAGATGTCATGCACGCATATTGGCTCCATCACGAGTAGAGCAGTTAGATGGACCTCACTGTCTTTC

Reverse complement sequence

GAAAGACAGTGAGGTCCATCTAACTGCTCTACTCGTGATGGAGCCAATATGCGTGCATGACATCTTATCATCCCCACCGTGTGAATGTCTCCTCGGCAAG[C/T]
TGCCATGCTCAGCGCAGCGTACTCCCTCCGTCCCAATAAGAACCAATTCCTGGCTATGAATATGGACATATGCACATATCCATATTCATAGCCAGGAATT

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	53.10%	46.90%	0.02%	0.00%	NA
All Indica	2759	52.60%	47.40%	0.04%	0.00%	NA
All Japonica	1512	44.80%	55.20%	0.00%	0.00%	NA
Aus	269	87.40%	12.60%	0.00%	0.00%	NA
Indica I	595	21.50%	78.50%	0.00%	0.00%	NA
Indica II	465	63.70%	36.10%	0.22%	0.00%	NA
Indica III	913	65.70%	34.30%	0.00%	0.00%	NA
Indica Intermediate	786	54.30%	45.70%	0.00%	0.00%	NA
Temperate Japonica	767	76.00%	24.00%	0.00%	0.00%	NA
Tropical Japonica	504	5.00%	95.00%	0.00%	0.00%	NA
Japonica Intermediate	241	29.00%	71.00%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	61.10%	38.90%	0.00%	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
vg1221121568	G -> A	LOC_Os12g34790.1	upstream_gene_variant ; 1351.0bp to feature; MODIFIER	silent_mutation	Average:75.128; most accessible tissue: Zhenshan97 flower, score: 91.257	N	N	N	N
vg1221121568	G -> A	LOC_Os12g34780-LOC_Os12g34790	intergenic_region ; MODIFIER	silent_mutation	Average:75.128; most accessible tissue: Zhenshan97 flower, score: 91.257	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)
vg1221121568	G	A	0.0	0.2	0.08	-0.02	0.24	0.23

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221121568	NA	4.18E-17	Grain_length	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1221121568	NA	2.17E-08	mr1189_2	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
vg1221121568	NA	1.49E-09	mr1338_2	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
vg1221121568	NA	4.98E-06	mr1383_2	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
vg1221121568	NA	6.46E-08	mr1446_2	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
vg1221121568	NA	1.31E-09	mr1530_2	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
vg1221121568	4.89E-06	NA	mr1613_2	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
vg1221121568	9.55E-06	NA	mr1795_2	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
vg1221121568	NA	6.92E-07	mr1895_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
vg1221121568	NA	9.19E-07	mr1980_2	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