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Detailed information for vg0908611714:

Variant ID: vg0908611714 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 8611714
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAAATAAAGATCACCAGGTTTTAGAGATAAGATTCATTTCAGGTTACAGCGCAGCTGATAACGGCAGCTAGAATAATGGCAGTTGCTGCTGATGACTCT[A/T]
CATGTGTATTTAGGGATAAAAACGGATCGGATATTTTCTTGACCGTTCAGCCGTTTCTACCAAATATGGCAAGTATTTTTTCTAACACCAGGAATATTAA

Reverse complement sequence

TTAATATTCCTGGTGTTAGAAAAAATACTTGCCATATTTGGTAGAAACGGCTGAACGGTCAAGAAAATATCCGATCCGTTTTTATCCCTAAATACACATG[T/A]
AGAGTCATCAGCAGCAACTGCCATTATTCTAGCTGCCGTTATCAGCTGCGCTGTAACCTGAAATGAATCTTATCTCTAAAACCTGGTGATCTTTATTTTC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.80%	2.80%	2.45%	0.00%	NA
All Indica	2759	91.10%	4.70%	4.13%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	86.40%	1.50%	12.10%	0.00%	NA
Indica II	465	98.30%	0.90%	0.86%	0.00%	NA
Indica III	913	89.60%	9.30%	1.10%	0.00%	NA
Indica Intermediate	786	92.20%	4.20%	3.56%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	0.00%	2.22%	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
vg0908611714	A -> T	LOC_Os09g14540.1	upstream_gene_variant ; 2440.0bp to feature; MODIFIER	silent_mutation	Average:56.292; most accessible tissue: Callus, score: 74.295	N	N	N	N
vg0908611714	A -> T	LOC_Os09g14550.1	upstream_gene_variant ; 1689.0bp to feature; MODIFIER	silent_mutation	Average:56.292; most accessible tissue: Callus, score: 74.295	N	N	N	N
vg0908611714	A -> T	LOC_Os09g14540-LOC_Os09g14550	intergenic_region ; MODIFIER	silent_mutation	Average:56.292; most accessible tissue: Callus, score: 74.295	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0908611714	7.72E-07	7.72E-07	mr1523_2	Ind_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
vg0908611714	NA	7.56E-07	mr1713_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