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Detailed information for vg0906112223:

Variant ID: vg0906112223 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6112223
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.67, C: 0.33, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

AAGATGCTCAATTATATACCGTTTATCATGCAATCCGAAGAAGGCAAGATCACTGGTAGAGAAACCCTTTTTACTCCCGTTTGGGAACCCCCTTTAGTCC[T/C]
GGGTTTCCAACCGGGAGTAGCAATCCGAGACTAAAGATGCCCATCTTTAGTCCCGGTTGAAATAACCGGGACTAAAGATGGATCTTTAGTCAGATAGGAT

Reverse complement sequence

ATCCTATCTGACTAAAGATCCATCTTTAGTCCCGGTTATTTCAACCGGGACTAAAGATGGGCATCTTTAGTCTCGGATTGCTACTCCCGGTTGGAAACCC[A/G]
GGACTAAAGGGGGTTCCCAAACGGGAGTAAAAAGGGTTTCTCTACCAGTGATCTTGCCTTCTTCGGATTGCATGATAAACGGTATATAATTGAGCATCTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.70%	20.00%	0.19%	1.06%	NA
All Indica	2759	83.30%	14.70%	0.29%	1.74%	NA
All Japonica	1512	76.50%	23.50%	0.00%	0.00%	NA
Aus	269	54.60%	45.00%	0.00%	0.37%	NA
Indica I	595	76.50%	19.80%	0.50%	3.19%	NA
Indica II	465	92.90%	6.50%	0.00%	0.65%	NA
Indica III	913	85.40%	12.00%	0.33%	2.19%	NA
Indica Intermediate	786	80.30%	18.70%	0.25%	0.76%	NA
Temperate Japonica	767	89.70%	10.30%	0.00%	0.00%	NA
Tropical Japonica	504	65.70%	34.30%	0.00%	0.00%	NA
Japonica Intermediate	241	56.80%	43.20%	0.00%	0.00%	NA
VI/Aromatic	96	50.00%	50.00%	0.00%	0.00%	NA
Intermediate	90	78.90%	18.90%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906112223	T -> DEL	N	N	silent_mutation	Average:52.56; most accessible tissue: Zhenshan97 flag leaf, score: 70.007	N	N	N	N
vg0906112223	T -> C	LOC_Os09g11020.1	downstream_gene_variant ; 4790.0bp to feature; MODIFIER	silent_mutation	Average:52.56; most accessible tissue: Zhenshan97 flag leaf, score: 70.007	N	N	N	N
vg0906112223	T -> C	LOC_Os09g11010-LOC_Os09g11020	intergenic_region ; MODIFIER	silent_mutation	Average:52.56; most accessible tissue: Zhenshan97 flag leaf, score: 70.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906112223	9.20E-07	9.43E-06	mr1160_2	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