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Detailed information for vg1217387481:

Variant ID: vg1217387481 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17387481
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

AGCCGCCACGTAGCACTTCTACAAACGCTGCTACGCCGCCACGTAGTATTTTAATAAATTAGAAAAAATCACAAAAATTACGAGAATAAATAAAACATCC[G/A]
GATATCGACATTCACTAATATACGGTGGACCCATTGTGTTTACGTACCTCTCCACCTATTACCTTTCTCTCCTATTTTCCTGTTTTGTTAGATGGAAAAA

Reverse complement sequence

TTTTTCCATCTAACAAAACAGGAAAATAGGAGAGAAAGGTAATAGGTGGAGAGGTACGTAAACACAATGGGTCCACCGTATATTAGTGAATGTCGATATC[C/T]
GGATGTTTTATTTATTCTCGTAATTTTTGTGATTTTTTCTAATTTATTAAAATACTACGTGGCGGCGTAGCAGCGTTTGTAGAAGTGCTACGTGGCGGCT

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	41.00%	32.10%	1.93%	24.93%	NA
All Indica	2759	16.70%	49.90%	2.75%	30.63%	NA
All Japonica	1512	81.50%	7.80%	0.60%	10.12%	NA
Aus	269	68.00%	0.70%	0.74%	30.48%	NA
Indica I	595	3.20%	83.40%	0.84%	12.61%	NA
Indica II	465	21.70%	53.10%	2.80%	22.37%	NA
Indica III	913	25.40%	26.70%	3.18%	44.69%	NA
Indica Intermediate	786	14.00%	49.50%	3.69%	32.82%	NA
Temperate Japonica	767	95.20%	3.50%	0.91%	0.39%	NA
Tropical Japonica	504	60.50%	12.30%	0.40%	26.79%	NA
Japonica Intermediate	241	81.70%	12.00%	0.00%	6.22%	NA
VI/Aromatic	96	18.80%	4.20%	0.00%	77.08%	NA
Intermediate	90	48.90%	20.00%	4.44%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217387481	G -> DEL	N	N	silent_mutation	Average:23.212; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1217387481	G -> A	LOC_Os12g29330.1	upstream_gene_variant ; 3861.0bp to feature; MODIFIER	silent_mutation	Average:23.212; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1217387481	G -> A	LOC_Os12g29320-LOC_Os12g29330	intergenic_region ; MODIFIER	silent_mutation	Average:23.212; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217387481	NA	1.67E-12	mr1018	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
vg1217387481	NA	3.23E-08	mr1019	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
vg1217387481	NA	2.18E-11	mr1132	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
vg1217387481	NA	1.59E-09	mr1707	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
vg1217387481	1.51E-06	4.96E-12	mr1019_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
vg1217387481	NA	4.31E-12	mr1055_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
vg1217387481	6.74E-08	2.11E-16	mr1132_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
vg1217387481	NA	3.32E-13	mr1178_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
vg1217387481	NA	8.67E-09	mr1261_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
vg1217387481	NA	1.90E-14	mr1390_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
vg1217387481	NA	6.78E-15	mr1490_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
vg1217387481	NA	1.33E-09	mr1707_2	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
vg1217387481	5.08E-07	NA	mr1778_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
vg1217387481	NA	1.67E-08	mr1860_2	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