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Detailed information for vg0406472365:

Variant ID: vg0406472365 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6472365
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

TCGTCGTCGGCATGACGTGGAACCACGTCGTCGCCGACGGCAAGGGCATAGCTCAGTTCCTGCGTGCCGTCGGCGAGCTCGCGCGGGGGCTGCCGCGGCC[G/A]
TCCGTCCTGCCGGTGAGCTGCGGCGACGACTCCCTCCCGGAGCTCCCGCCGCTGGTCGCCGCCATGGAGAAGGCGATGCTGACGCAGGAGAGCAAGCAGT

Reverse complement sequence

ACTGCTTGCTCTCCTGCGTCAGCATCGCCTTCTCCATGGCGGCGACCAGCGGCGGGAGCTCCGGGAGGGAGTCGTCGCCGCAGCTCACCGGCAGGACGGA[C/T]
GGCCGCGGCAGCCCCCGCGCGAGCTCGCCGACGGCACGCAGGAACTGAGCTATGCCCTTGCCGTCGGCGACGACGTGGTTCCACGTCATGCCGACGACGA

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	65.10%	34.90%	0.00%	0.00%	NA
All Indica	2759	42.70%	57.30%	0.00%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	9.40%	90.60%	0.00%	0.00%	NA
Indica II	465	53.30%	46.70%	0.00%	0.00%	NA
Indica III	913	57.30%	42.70%	0.00%	0.00%	NA
Indica Intermediate	786	44.70%	55.30%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	59.40%	40.60%	0.00%	0.00%	NA
Intermediate	90	75.60%	24.40%	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
vg0406472365	G -> A	LOC_Os04g11810.1	synonymous_variant ; p.Pro189Pro; LOW	synonymous_codon	Average:72.179; most accessible tissue: Minghui63 root, score: 83.807	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406472365	NA	2.54E-16	mr1143	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
vg0406472365	NA	1.02E-06	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
vg0406472365	NA	1.37E-06	mr1045_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
vg0406472365	NA	3.08E-10	mr1062_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
vg0406472365	NA	2.72E-19	mr1195_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
vg0406472365	NA	2.19E-06	mr1358_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
vg0406472365	NA	2.37E-07	mr1517_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
vg0406472365	NA	1.12E-32	mr1598_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
vg0406472365	NA	8.51E-07	mr1655_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
vg0406472365	NA	2.18E-09	mr1715_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
vg0406472365	1.34E-06	7.91E-08	mr1882_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
vg0406472365	NA	1.73E-07	mr1882_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
vg0406472365	NA	3.16E-06	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
vg0406472365	NA	2.67E-06	mr1925_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