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Detailed information for vg0802209035:

Variant ID: vg0802209035 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 2209035
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.67, A: 0.32, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

CTTAAGATGAAAGAAGCAAATGATCGATGGGATATCATCATGAATGTTTGGATGGAGATGCTTTGCTACATGGCATTTCACTGCGGACCTGGTTTCCACA[T/A]
TAAGCAGGTAAGCAAGGGTGGAGAGTTCATCAGCCATGCATGTGAAGGTTGTGATATATAATCTAGGCTTTCCATATTCAACATATTCACCTGAAACCGA

Reverse complement sequence

TCGGTTTCAGGTGAATATGTTGAATATGGAAAGCCTAGATTATATATCACAACCTTCACATGCATGGCTGATGAACTCTCCACCCTTGCTTACCTGCTTA[A/T]
TGTGGAAACCAGGTCCGCAGTGAAATGCCATGTAGCAAAGCATCTCCATCCAAACATTCATGATGATATCCCATCGATCATTTGCTTCTTTCATCTTAAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.90%	40.80%	0.08%	0.30%	NA
All Indica	2759	38.30%	61.10%	0.14%	0.47%	NA
All Japonica	1512	98.30%	1.70%	0.00%	0.00%	NA
Aus	269	34.20%	65.80%	0.00%	0.00%	NA
Indica I	595	38.80%	60.70%	0.17%	0.34%	NA
Indica II	465	15.50%	84.10%	0.22%	0.22%	NA
Indica III	913	41.80%	57.70%	0.22%	0.22%	NA
Indica Intermediate	786	47.30%	51.70%	0.00%	1.02%	NA
Temperate Japonica	767	98.30%	1.70%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.50%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	62.20%	36.70%	0.00%	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
vg0802209035	T -> A	LOC_Os08g04490.1	missense_variant ; p.Ile669Asn; MODERATE	nonsynonymous_codon ; I669N	Average:59.437; most accessible tissue: Callus, score: 77.311	unknown	unknown	TOLERATED	0.08
vg0802209035	T -> DEL	LOC_Os08g04490.1	N	frameshift_variant	Average:59.437; most accessible tissue: Callus, score: 77.311	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0802209035	NA	1.43E-06	mr1011	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
vg0802209035	NA	3.65E-07	mr1593	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
vg0802209035	4.45E-32	2.38E-30	mr1739	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
vg0802209035	9.72E-37	1.13E-65	mr1739	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
vg0802209035	NA	1.10E-06	mr1268_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
vg0802209035	3.40E-36	3.60E-29	mr1739_2	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
vg0802209035	1.79E-43	6.86E-76	mr1739_2	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