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Detailed information for vg1217798287:

Variant ID: vg1217798287 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17798287
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

TACACAGTACGATGCAGATACTCATAATGCATGCGCACTTACCCCTATAAACGCATGCACGCAAACCCTACCCCTATGATCACATTCGAAGAGTAGGCCG[G/A]
CAAATCCTTGAAATTGACGAAGTCACCATAGGCACCTCGTTGTTGCCTACCACTGAAAGCACACCGCCATTAAATCCTGGAAAATTTGCTCCTATCACTG

Reverse complement sequence

CAGTGATAGGAGCAAATTTTCCAGGATTTAATGGCGGTGTGCTTTCAGTGGTAGGCAACAACGAGGTGCCTATGGTGACTTCGTCAATTTCAAGGATTTG[C/T]
CGGCCTACTCTTCGAATGTGATCATAGGGGTAGGGTTTGCGTGCATGCGTTTATAGGGGTAAGTGCGCATGCATTATGAGTATCTGCATCGTACTGTGTA

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	52.70%	14.30%	0.57%	32.46%	NA
All Indica	2759	43.30%	23.70%	0.51%	32.48%	NA
All Japonica	1512	69.00%	0.50%	0.33%	30.22%	NA
Aus	269	61.00%	0.70%	1.86%	36.43%	NA
Indica I	595	61.50%	36.30%	0.17%	2.02%	NA
Indica II	465	26.50%	14.60%	0.86%	58.06%	NA
Indica III	913	41.70%	16.00%	0.11%	42.17%	NA
Indica Intermediate	786	41.50%	28.40%	1.02%	29.13%	NA
Temperate Japonica	767	95.80%	0.40%	0.00%	3.78%	NA
Tropical Japonica	504	39.10%	0.40%	0.99%	59.52%	NA
Japonica Intermediate	241	46.10%	0.80%	0.00%	53.11%	NA
VI/Aromatic	96	37.50%	1.00%	2.08%	59.38%	NA
Intermediate	90	56.70%	13.30%	1.11%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217798287	G -> DEL	N	N	silent_mutation	Average:28.919; most accessible tissue: Zhenshan97 root, score: 56.557	N	N	N	N
vg1217798287	G -> A	LOC_Os12g29780.1	upstream_gene_variant ; 3829.0bp to feature; MODIFIER	silent_mutation	Average:28.919; most accessible tissue: Zhenshan97 root, score: 56.557	N	N	N	N
vg1217798287	G -> A	LOC_Os12g29760-LOC_Os12g29780	intergenic_region ; MODIFIER	silent_mutation	Average:28.919; most accessible tissue: Zhenshan97 root, score: 56.557	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217798287	NA	1.46E-08	mr1180	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
vg1217798287	NA	5.78E-07	mr1183	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
vg1217798287	NA	5.80E-06	mr1327	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
vg1217798287	NA	1.83E-06	mr1336	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
vg1217798287	NA	5.63E-07	mr1503	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
vg1217798287	NA	1.49E-07	mr1579	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