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Detailed information for vg0329230827:

Variant ID: vg0329230827 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 29230827
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: 119. )

Flanking Sequence (100 bp) in Reference Genome:

TTTAGAGACCCAAAGTTTATAAGTCAAAAGTTTATATATCCGATTCAAATTTGAATTTGTATTCAAATATTTTTATATATAGTATTTCTATACATCTAAA[G/A]
TTTATACACCTAAAGTTTATAGAGACAAAGTTTATAAGTCAAAAGTTTATATATCCGATTCAAATTTGAATTTGAATTCAAATATTTTTATATATAGTAT

Reverse complement sequence

ATACTATATATAAAAATATTTGAATTCAAATTCAAATTTGAATCGGATATATAAACTTTTGACTTATAAACTTTGTCTCTATAAACTTTAGGTGTATAAA[C/T]
TTTAGATGTATAGAAATACTATATATAAAAATATTTGAATACAAATTCAAATTTGAATCGGATATATAAACTTTTGACTTATAAACTTTGGGTCTCTAAA

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	84.70%	6.50%	8.70%	0.15%	NA
All Indica	2759	74.20%	10.80%	14.68%	0.25%	NA
All Japonica	1512	99.60%	0.10%	0.33%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	75.30%	7.40%	16.97%	0.34%	NA
Indica II	465	73.50%	11.80%	14.41%	0.22%	NA
Indica III	913	82.90%	9.30%	7.67%	0.11%	NA
Indica Intermediate	786	63.70%	14.60%	21.25%	0.38%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.60%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	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
vg0329230827	G -> A	LOC_Os03g51100-LOC_Os03g51110	intergenic_region ; MODIFIER	silent_mutation	Average:21.067; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0329230827	G -> DEL	N	N	silent_mutation	Average:21.067; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0329230827	2.19E-06	8.05E-06	mr1833	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
vg0329230827	7.15E-06	2.08E-07	mr1833	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