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Detailed information for vg0327937122:

Variant ID: vg0327937122 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 27937122
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: 300. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTACTAAAAGGACTGAAGAGAAGGGTTTAGGGGAGCAGGAGCAGTCACTTGCTGTTGTGGTTGCTCCGGAACCAACGGTCCCACCGGAAGGTAGTTCC[G/A]
ACAGCGACGTAGGTGACGAAGACGAGGAGTGCTCGTCGCCAAGCGATCCTTGTCCAAGCCCAAGCCCGAAGAGAAGGAAAAAGGGCGACGGTGAAGAAGG

Reverse complement sequence

CCTTCTTCACCGTCGCCCTTTTTCCTTCTCTTCGGGCTTGGGCTTGGACAAGGATCGCTTGGCGACGAGCACTCCTCGTCTTCGTCACCTACGTCGCTGT[C/T]
GGAACTACCTTCCGGTGGGACCGTTGGTTCCGGAGCAACCACAACAGCAAGTGACTGCTCCTGCTCCCCTAAACCCTTCTCTTCAGTCCTTTTAGTACTA

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	88.80%	10.10%	1.12%	0.00%	NA
All Indica	2759	81.50%	16.60%	1.88%	0.00%	NA
All Japonica	1512	99.60%	0.40%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	52.70%	40.90%	6.45%	0.00%	NA
Indica III	913	85.50%	14.50%	0.00%	0.00%	NA
Indica Intermediate	786	80.00%	17.20%	2.80%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	12.20%	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
vg0327937122	G -> A	LOC_Os03g49040.1	missense_variant ; p.Asp37Asn; MODERATE	nonsynonymous_codon ; D37N	Average:27.888; most accessible tissue: Minghui63 panicle, score: 46.754	benign	0.091	TOLERATED	0.27

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0327937122	NA	6.88E-06	mr1064	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
vg0327937122	NA	1.70E-06	mr1122	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
vg0327937122	NA	3.93E-07	mr1193	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
vg0327937122	NA	2.68E-06	mr1297	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
vg0327937122	NA	7.74E-06	mr1297	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
vg0327937122	NA	1.72E-06	mr1432	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
vg0327937122	NA	9.38E-06	mr1433	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
vg0327937122	NA	1.08E-06	mr1537	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
vg0327937122	NA	6.50E-07	mr1821	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
vg0327937122	NA	4.50E-07	mr1968	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
vg0327937122	NA	1.97E-06	mr1193_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
vg0327937122	NA	6.00E-06	mr1720_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