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Detailed information for vg1216550375:

Variant ID: vg1216550375 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16550375
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: 0.01, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

TAATAGTAGTTCTAGTAAATATATTCAGTTATTGATTTGATGGCACTAATTTATAGTATTATAAATATTATTATATTTGTCTATAAACTTAGTCAAATTT[G/A]
AAATAGTTTAAGTTTAACCAAAGTCAAAACGTGTTGTAACCTGAAACAAAGGGAGTGGTATATATGAAGTATGGACAGAGCAACATGATCACCAAAACAC

Reverse complement sequence

GTGTTTTGGTGATCATGTTGCTCTGTCCATACTTCATATATACCACTCCCTTTGTTTCAGGTTACAACACGTTTTGACTTTGGTTAAACTTAAACTATTT[C/T]
AAATTTGACTAAGTTTATAGACAAATATAATAATATTTATAATACTATAAATTAGTGCCATCAAATCAATAACTGAATATATTTACTAGAACTACTATTA

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	69.50%	25.60%	1.04%	3.87%	NA
All Indica	2759	64.50%	32.00%	1.63%	1.88%	NA
All Japonica	1512	81.90%	18.10%	0.07%	0.00%	NA
Aus	269	49.80%	1.10%	0.74%	48.33%	NA
Indica I	595	38.20%	55.80%	4.37%	1.68%	NA
Indica II	465	58.90%	38.70%	0.86%	1.51%	NA
Indica III	913	85.80%	12.90%	0.44%	0.88%	NA
Indica Intermediate	786	63.10%	32.10%	1.40%	3.44%	NA
Temperate Japonica	767	99.30%	0.50%	0.13%	0.00%	NA
Tropical Japonica	504	50.40%	49.60%	0.00%	0.00%	NA
Japonica Intermediate	241	92.10%	7.90%	0.00%	0.00%	NA
VI/Aromatic	96	74.00%	25.00%	0.00%	1.04%	NA
Intermediate	90	68.90%	30.00%	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
vg1216550375	G -> DEL	N	N	silent_mutation	Average:35.606; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg1216550375	G -> A	LOC_Os12g28050-LOC_Os12g28065	intergenic_region ; MODIFIER	silent_mutation	Average:35.606; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216550375	NA	3.03E-06	mr1382	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
vg1216550375	NA	9.43E-07	mr1471	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
vg1216550375	NA	2.35E-07	mr1551	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
vg1216550375	NA	4.87E-09	mr1696	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
vg1216550375	NA	3.82E-06	mr1700	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
vg1216550375	NA	9.36E-07	mr1925	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
vg1216550375	5.33E-06	NA	mr1022_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
vg1216550375	2.88E-07	NA	mr1023_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
vg1216550375	NA	5.33E-08	mr1047_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
vg1216550375	7.21E-06	NA	mr1055_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
vg1216550375	4.49E-08	NA	mr1079_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
vg1216550375	2.46E-07	NA	mr1132_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
vg1216550375	NA	7.87E-07	mr1257_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
vg1216550375	1.87E-07	NA	mr1390_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
vg1216550375	2.77E-07	NA	mr1489_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
vg1216550375	2.31E-08	NA	mr1490_2	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
vg1216550375	NA	7.91E-10	mr1642_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
vg1216550375	NA	5.79E-06	mr1782_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
vg1216550375	NA	5.66E-09	mr1808_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
vg1216550375	NA	3.60E-06	mr1815_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
vg1216550375	NA	7.23E-06	mr1892_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