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Detailed information for vg0727008459:

Variant ID: vg0727008459 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 27008459
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:

TTCTACCGTTGAATTTGATTCATCATGGTGACGATGATGTACATAGGTGTTTTGATTGGAGTACGATGTGTAAAAAATTAGGGTGGTGAGATCAGAAGTG[G/A]
GTGGTGCACTTTGCAAATGTGTATGTACTATATGCTTTGATGTTGATATATCATACAAGAACACACACATTCAGGGGGGCAAACATCGGTCCATAGCTTT

Reverse complement sequence

AAAGCTATGGACCGATGTTTGCCCCCCTGAATGTGTGTGTTCTTGTATGATATATCAACATCAAAGCATATAGTACATACACATTTGCAAAGTGCACCAC[C/T]
CACTTCTGATCTCACCACCCTAATTTTTTACACATCGTACTCCAATCAAAACACCTATGTACATCATCGTCACCATGATGAATCAAATTCAACGGTAGAA

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	94.10%	4.90%	0.99%	0.00%	NA
All Indica	2759	97.40%	2.30%	0.33%	0.00%	NA
All Japonica	1512	86.60%	11.00%	2.45%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.60%	1.50%	0.84%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	98.10%	1.90%	0.00%	0.00%	NA
Indica Intermediate	786	94.90%	4.60%	0.51%	0.00%	NA
Temperate Japonica	767	73.90%	21.50%	4.56%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	0.40%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg0727008459	G -> A	LOC_Os07g45260.1	3_prime_UTR_variant ; 553.0bp to feature; MODIFIER	silent_mutation	Average:60.928; most accessible tissue: Zhenshan97 root, score: 86.14	N	N	N	N
vg0727008459	G -> A	LOC_Os07g45250.1	downstream_gene_variant ; 4145.0bp to feature; MODIFIER	silent_mutation	Average:60.928; most accessible tissue: Zhenshan97 root, score: 86.14	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0727008459	NA	7.70E-07	mr1062	Jap_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
vg0727008459	2.77E-06	1.01E-08	mr1915	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