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Detailed information for vg0314514506:

Variant ID: vg0314514506 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14514506
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, A: 0.01, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

GACCGCAATTAAGCTACTCTGAAGAAACGAACTGAACTCCGCCTGCATGGAACTTGCAAGCACAGTCATCATAGACCTCTGATAATTTCTACCGACAGCA[G/A]
TCTCCTGTTACTAATCTGGAAATTTTGAGCAGGCGGAGCAAGTCCTGGGATGTCGCGGATGTTCTTGTTATGTGGGTTGACAATCTGTTAAAAAAATAAA

Reverse complement sequence

TTTATTTTTTTAACAGATTGTCAACCCACATAACAAGAACATCCGCGACATCCCAGGACTTGCTCCGCCTGCTCAAAATTTCCAGATTAGTAACAGGAGA[C/T]
TGCTGTCGGTAGAAATTATCAGAGGTCTATGATGACTGTGCTTGCAAGTTCCATGCAGGCGGAGTTCAGTTCGTTTCTTCAGAGTAGCTTAATTGCGGTC

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	78.80%	21.00%	0.11%	0.13%	NA
All Indica	2759	67.20%	32.40%	0.18%	0.22%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	72.10%	27.90%	0.00%	0.00%	NA
Indica I	595	46.60%	53.10%	0.00%	0.34%	NA
Indica II	465	52.50%	47.30%	0.00%	0.22%	NA
Indica III	913	84.80%	15.10%	0.11%	0.00%	NA
Indica Intermediate	786	71.10%	28.00%	0.51%	0.38%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	80.00%	20.00%	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
vg0314514506	G -> A	LOC_Os03g25390.2	synonymous_variant ; p.Leu306Leu; LOW	synonymous_codon	Average:70.811; most accessible tissue: Callus, score: 91.512	N	N	N	N
vg0314514506	G -> A	LOC_Os03g25390.1	synonymous_variant ; p.Leu266Leu; LOW	synonymous_codon	Average:70.811; most accessible tissue: Callus, score: 91.512	N	N	N	N
vg0314514506	G -> DEL	LOC_Os03g25390.2	N	frameshift_variant	Average:70.811; most accessible tissue: Callus, score: 91.512	N	N	N	N
vg0314514506	G -> DEL	LOC_Os03g25390.1	N	frameshift_variant	Average:70.811; most accessible tissue: Callus, score: 91.512	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314514506	1.93E-25	1.50E-43	mr1542	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
vg0314514506	1.18E-20	2.58E-18	mr1542	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
vg0314514506	5.19E-28	7.80E-51	mr1542_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
vg0314514506	3.83E-25	2.34E-21	mr1542_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
vg0314514506	4.20E-10	NA	mr1587_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
vg0314514506	6.92E-08	NA	mr1587_2	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