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Detailed information for vg0315272708:

Variant ID: vg0315272708 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 15272708
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTATTTACTCGGATGTTACACCACATATGCCATATATTTCCAGGTGTGGTGAGACCATGTGTCTTTTAGGGACTTCAGCACATCTGTTAAAGCAGTGT[G/A]
CGCATGGTGTGTGCCCAATACTTTGAAAATTTCTTTATTCACAACACACAAGCTTCTTTATAGCTGTTTGGCCATGTGAACTTTCAATGATGAAGTCGAC

Reverse complement sequence

GTCGACTTCATCATTGAAAGTTCACATGGCCAAACAGCTATAAAGAAGCTTGTGTGTTGTGAATAAAGAAATTTTCAAAGTATTGGGCACACACCATGCG[C/T]
ACACTGCTTTAACAGATGTGCTGAAGTCCCTAAAAGACACATGGTCTCACCACACCTGGAAATATATGGCATATGTGGTGTAACATCCGAGTAAATAAAC

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	46.60%	0.10%	4.78%	48.56%	NA
All Indica	2759	20.70%	0.20%	7.50%	71.62%	NA
All Japonica	1512	80.50%	0.00%	0.99%	18.52%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	16.50%	0.20%	4.71%	78.66%	NA
Indica II	465	12.90%	0.40%	9.03%	77.63%	NA
Indica III	913	26.50%	0.20%	7.67%	65.61%	NA
Indica Intermediate	786	21.80%	0.00%	8.52%	69.72%	NA
Temperate Japonica	767	96.50%	0.00%	0.13%	3.39%	NA
Tropical Japonica	504	57.90%	0.00%	1.79%	40.28%	NA
Japonica Intermediate	241	76.80%	0.00%	2.07%	21.16%	NA
VI/Aromatic	96	92.70%	0.00%	0.00%	7.29%	NA
Intermediate	90	61.10%	0.00%	4.44%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0315272708	G -> A	LOC_Os03g26750-LOC_Os03g26760	intergenic_region ; MODIFIER	silent_mutation	Average:22.748; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0315272708	G -> DEL	N	N	silent_mutation	Average:22.748; 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
vg0315272708	NA	2.66E-06	mr1468	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
vg0315272708	4.70E-06	NA	mr1860	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
vg0315272708	NA	7.82E-07	mr1860	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