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Detailed information for vg0915181122:

Variant ID: vg0915181122 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 15181122
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

CTCGTTTTAGTCTAATCGTGCGACGCACCTCCGACCGTCCGATCTCATTATCTATTTATTTTCGGCTTACGTTATCGCTTTCTCCACTAGTATTTGACTG[C/T]
AGAGAGGCTGACACACCCACGTAGTAGGAAGGACTGAGATAGACATGTATGCCTTTTTTCTCTTCAAATAAAATTTTCTCTCAAATTACTTATCCGATCT

Reverse complement sequence

AGATCGGATAAGTAATTTGAGAGAAAATTTTATTTGAAGAGAAAAAAGGCATACATGTCTATCTCAGTCCTTCCTACTACGTGGGTGTGTCAGCCTCTCT[G/A]
CAGTCAAATACTAGTGGAGAAAGCGATAACGTAAGCCGAAAATAAATAGATAATGAGATCGGACGGTCGGAGGTGCGTCGCACGATTAGACTAAAACGAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.10%	19.70%	0.23%	0.00%	NA
All Indica	2759	66.40%	33.20%	0.40%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	67.20%	32.60%	0.17%	0.00%	NA
Indica II	465	47.30%	52.30%	0.43%	0.00%	NA
Indica III	913	76.00%	23.50%	0.44%	0.00%	NA
Indica Intermediate	786	66.00%	33.50%	0.51%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	13.30%	0.00%	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
vg0915181122	C -> T	LOC_Os09g25330-LOC_Os09g25340	intergenic_region ; MODIFIER	silent_mutation	Average:46.454; most accessible tissue: Zhenshan97 root, score: 76.397	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0915181122	6.94E-06	NA	mr1180	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
vg0915181122	NA	5.55E-06	mr1963	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