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Detailed information for vg1014712704:

Variant ID: vg1014712704 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 14712704
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGTTAACGATGTTAAATATTTAGAAACGGAGGGAGTATATCTTAACTAATTAAAATATTCGTAATTTTCCATTCATCACAAGACGGACGTCTTCGTCC[G/A]
TCGGCGGTGCGCCTTCACAGCCCCCGAATCCCGATCGCTCTTAGAATCGGAAACAGGGAAACACTTCCCAAAATCGGCACAACCAAAACTCAACCACTCT

Reverse complement sequence

AGAGTGGTTGAGTTTTGGTTGTGCCGATTTTGGGAAGTGTTTCCCTGTTTCCGATTCTAAGAGCGATCGGGATTCGGGGGCTGTGAAGGCGCACCGCCGA[C/T]
GGACGAAGACGTCCGTCTTGTGATGAATGGAAAATTACGAATATTTTAATTAGTTAAGATATACTCCCTCCGTTTCTAAATATTTAACATCGTTAACTTT

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	92.30%	5.70%	1.99%	0.00%	NA
All Indica	2759	99.60%	0.10%	0.22%	0.00%	NA
All Japonica	1512	78.30%	16.30%	5.42%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.40%	0.51%	0.00%	NA
Temperate Japonica	767	76.00%	15.60%	8.34%	0.00%	NA
Tropical Japonica	504	84.10%	14.70%	1.19%	0.00%	NA
Japonica Intermediate	241	73.40%	21.60%	4.98%	0.00%	NA
VI/Aromatic	96	86.50%	13.50%	0.00%	0.00%	NA
Intermediate	90	86.70%	6.70%	6.67%	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
vg1014712704	G -> A	LOC_Os10g28280.1	downstream_gene_variant ; 3191.0bp to feature; MODIFIER	silent_mutation	Average:69.207; most accessible tissue: Minghui63 panicle, score: 86.85	N	N	N	N
vg1014712704	G -> A	LOC_Os10g28290.1	intron_variant ; MODIFIER	silent_mutation	Average:69.207; most accessible tissue: Minghui63 panicle, score: 86.85	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1014712704	9.27E-06	9.27E-06	mr1253	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
vg1014712704	NA	7.21E-06	mr1648	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
vg1014712704	2.36E-06	2.36E-06	mr1899	Jap_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