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Detailed information for vg0314310040:

Variant ID: vg0314310040 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14310040
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: 313. )

Flanking Sequence (100 bp) in Reference Genome:

AAGAGGGGTGTGCTATCTGGTGGCCTAAACCAATGTATCCAAAACATATTCCTATTACTAAAGCGCATGCATCACTGATAGAATTCATCCCCGACTTTCA[G/A]
AAACTCACCGTTTGTTTAGATTGGGAATGGGAAACAAACTCCTTTCTAGCACAATAAATGGTACGGTGATCAAGTGCCAGGAGAGAATTTCCCTGCAATG

Reverse complement sequence

CATTGCAGGGAAATTCTCTCCTGGCACTTGATCACCGTACCATTTATTGTGCTAGAAAGGAGTTTGTTTCCCATTCCCAATCTAAACAAACGGTGAGTTT[C/T]
TGAAAGTCGGGGATGAATTCTATCAGTGATGCATGCGCTTTAGTAATAGGAATATGTTTTGGATACATTGGTTTAGGCCACCAGATAGCACACCCCTCTT

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	91.20%	7.90%	0.91%	0.00%	NA
All Indica	2759	85.40%	13.00%	1.56%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	87.70%	8.90%	3.36%	0.00%	NA
Indica II	465	92.30%	6.70%	1.08%	0.00%	NA
Indica III	913	80.70%	18.70%	0.55%	0.00%	NA
Indica Intermediate	786	85.00%	13.40%	1.65%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0314310040	G -> A	LOC_Os03g25060-LOC_Os03g25070	intergenic_region ; MODIFIER	silent_mutation	Average:47.014; most accessible tissue: Zhenshan97 young leaf, score: 66.83	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314310040	1.55E-06	NA	mr1542	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
vg0314310040	NA	9.93E-07	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
vg0314310040	NA	1.18E-06	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