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Detailed information for vg0109366509:

Variant ID: vg0109366509 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 9366509
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:

TTCGTGGGATTCCCATTGCGTCCAAAGTGCTAGCGAAGAGAAGATTGATGGAGCTGCCGCCATCGACGAGGACTCGCGCTACCTTGATATTCCGAATAGT[G/T]
GGTTCGACCACGATCGGATATCGTCCTGGTATAACAGCAGCCTTGGGGTAGTCTTCATCTAAGAACTCGATCTTCTGTTCAGACCACTTCATTTTGGGTG

Reverse complement sequence

CACCCAAAATGAAGTGGTCTGAACAGAAGATCGAGTTCTTAGATGAAGACTACCCCAAGGCTGCTGTTATACCAGGACGATATCCGATCGTGGTCGAACC[C/A]
ACTATTCGGAATATCAAGGTAGCGCGAGTCCTCGTCGATGGCGGCAGCTCCATCAATCTTCTCTTCGCTAGCACTTTGGACGCAATGGGAATCCCACGAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.90%	3.90%	0.21%	0.00%	NA
All Indica	2759	98.90%	1.00%	0.07%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	42.40%	54.60%	2.97%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	97.10%	2.80%	0.13%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0109366509	G -> T	LOC_Os01g16500.1	synonymous_variant ; p.Pro654Pro; LOW	synonymous_codon	Average:46.472; most accessible tissue: Zhenshan97 flag leaf, score: 61.926	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0109366509	2.55E-06	NA	mr1379	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