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Detailed information for vg0906772663:

Variant ID: vg0906772663 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6772663
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

GGTCCTCAACCAAGCACCTCAAGCAGAACAATGCCAAGACGCGCAGCGAAGAGTGATTCAAGTCATCACCAGATCTTATCCCTCCTCACAAGTGTCGAAA[C/T]
GGCAGAAGAAAATACAACTTCAGACAGTGCATAGCATTGTTTCGGCAGGTGATGGGGTCCCAAGATACTTGTCGCAGCCAATATCCATCGGGCTGGAGGA

Reverse complement sequence

TCCTCCAGCCCGATGGATATTGGCTGCGACAAGTATCTTGGGACCCCATCACCTGCCGAAACAATGCTATGCACTGTCTGAAGTTGTATTTTCTTCTGCC[G/A]
TTTCGACACTTGTGAGGAGGGATAAGATCTGGTGATGACTTGAATCACTCTTCGCTGCGCGTCTTGGCATTGTTCTGCTTGAGGTGCTTGGTTGAGGACC

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	84.30%	15.40%	0.25%	0.00%	NA
All Indica	2759	73.70%	25.90%	0.40%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	94.10%	5.90%	0.00%	0.00%	NA
Indica II	465	79.10%	20.20%	0.65%	0.00%	NA
Indica III	913	56.30%	42.80%	0.88%	0.00%	NA
Indica Intermediate	786	75.30%	24.70%	0.00%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	6.70%	1.11%	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
vg0906772663	C -> T	LOC_Os09g12020.1	downstream_gene_variant ; 297.0bp to feature; MODIFIER	silent_mutation	Average:59.305; most accessible tissue: Zhenshan97 young leaf, score: 85.364	N	N	N	N
vg0906772663	C -> T	LOC_Os09g12020-LOC_Os09g12050	intergenic_region ; MODIFIER	silent_mutation	Average:59.305; most accessible tissue: Zhenshan97 young leaf, score: 85.364	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906772663	NA	3.88E-06	mr1188	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
vg0906772663	NA	2.53E-06	mr1188_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