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Detailed information for vg0909064717:

Variant ID: vg0909064717 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9064717
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: 281. )

Flanking Sequence (100 bp) in Reference Genome:

CGCATCAGCTTGGGAGTTATCAGGAATATATCCTTCTGCATCCGCCGCTGCAGAACAGCATATCAGTGCTGCCATTACCAGTACCGGTTCGACTAAACCC[G/A]
TTCCAGGAAAACCACCAGTGCGCTGTAAAAGCAAGCACCGGCGCTGATGACACCACACCAGTCCCGGTTCAATAAAAAAACCCGGTACTAAGAGTTCATT

Reverse complement sequence

AATGAACTCTTAGTACCGGGTTTTTTTATTGAACCGGGACTGGTGTGGTGTCATCAGCGCCGGTGCTTGCTTTTACAGCGCACTGGTGGTTTTCCTGGAA[C/T]
GGGTTTAGTCGAACCGGTACTGGTAATGGCAGCACTGATATGCTGTTCTGCAGCGGCGGATGCAGAAGGATATATTCCTGATAACTCCCAAGCTGATGCG

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	88.70%	1.10%	0.38%	9.82%	NA
All Indica	2759	92.90%	0.00%	0.40%	6.67%	NA
All Japonica	1512	79.60%	3.40%	0.46%	16.53%	NA
Aus	269	97.40%	0.00%	0.00%	2.60%	NA
Indica I	595	94.80%	0.00%	0.00%	5.21%	NA
Indica II	465	98.10%	0.00%	0.22%	1.72%	NA
Indica III	913	87.80%	0.00%	0.44%	11.72%	NA
Indica Intermediate	786	94.30%	0.10%	0.76%	4.83%	NA
Temperate Japonica	767	69.60%	6.30%	0.78%	23.34%	NA
Tropical Japonica	504	93.10%	0.00%	0.20%	6.75%	NA
Japonica Intermediate	241	83.40%	1.20%	0.00%	15.35%	NA
VI/Aromatic	96	83.30%	0.00%	0.00%	16.67%	NA
Intermediate	90	92.20%	0.00%	0.00%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909064717	G -> DEL	N	N	silent_mutation	Average:76.213; most accessible tissue: Callus, score: 87.606	N	N	N	N
vg0909064717	G -> A	LOC_Os09g15030.1	upstream_gene_variant ; 1155.0bp to feature; MODIFIER	silent_mutation	Average:76.213; most accessible tissue: Callus, score: 87.606	N	N	N	N
vg0909064717	G -> A	LOC_Os09g15020-LOC_Os09g15030	intergenic_region ; MODIFIER	silent_mutation	Average:76.213; most accessible tissue: Callus, score: 87.606	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909064717	2.57E-06	NA	mr1010_2	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