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Detailed information for vg0905969651:

Variant ID: vg0905969651 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 5969651
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.84, T: 0.17, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

TTACTTGTGACTTATGTTTTTAAATTTTTTTAAAAACTTTTCAAATAAGATGGACGGTCAAAGTTGGGTGCGGAAAATCATGGCTGCACTTATAATAGGA[C/T]
GGAGGGAGTAGCACCTAGACACCCAGTTTGTGTTGATGATTGTCACGGACTCGTGTTGGGCTGGACATCCATGACGGACTACGGAAAAACTAATTCACGC

Reverse complement sequence

GCGTGAATTAGTTTTTCCGTAGTCCGTCATGGATGTCCAGCCCAACACGAGTCCGTGACAATCATCAACACAAACTGGGTGTCTAGGTGCTACTCCCTCC[G/A]
TCCTATTATAAGTGCAGCCATGATTTTCCGCACCCAACTTTGACCGTCCATCTTATTTGAAAAGTTTTTAAAAAAATTTAAAAACATAAGTCACAAGTAA

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	79.80%	19.90%	0.28%	0.00%	NA
All Indica	2759	69.40%	30.20%	0.40%	0.00%	NA
All Japonica	1512	97.80%	2.20%	0.00%	0.00%	NA
Aus	269	75.50%	24.50%	0.00%	0.00%	NA
Indica I	595	37.50%	62.00%	0.50%	0.00%	NA
Indica II	465	79.80%	20.20%	0.00%	0.00%	NA
Indica III	913	82.70%	17.00%	0.33%	0.00%	NA
Indica Intermediate	786	71.90%	27.50%	0.64%	0.00%	NA
Temperate Japonica	767	97.90%	2.10%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	95.90%	4.10%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	7.80%	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
vg0905969651	C -> T	LOC_Os09g10890.1	upstream_gene_variant ; 2325.0bp to feature; MODIFIER	silent_mutation	Average:50.432; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N
vg0905969651	C -> T	LOC_Os09g10880.1	downstream_gene_variant ; 3440.0bp to feature; MODIFIER	silent_mutation	Average:50.432; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N
vg0905969651	C -> T	LOC_Os09g10880-LOC_Os09g10890	intergenic_region ; MODIFIER	silent_mutation	Average:50.432; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0905969651	NA	5.65E-06	mr1598	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
vg0905969651	NA	7.38E-06	mr1170_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
vg0905969651	3.81E-06	3.81E-06	mr1520_2	Jap_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