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Detailed information for vg0622322008:

Variant ID: vg0622322008 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 22322008
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

GAAGACTAGGGCGACGACCACAGGCACTTGACGGCAGGCACGAGCTAGACACCAACGCCATCATCCTCCAGGAACTCCTCTTCTAGGTTGGGGAAAAAAT[G/A]
AGCAAGATTGAGTACAACCACCGTACTCAGCAAGACACACCCACAATTGCAGAATAAATGTGAAGGAGTATAAGGGGGTTATAATATAGGGGTTAGGATT

Reverse complement sequence

AATCCTAACCCCTATATTATAACCCCCTTATACTCCTTCACATTTATTCTGCAATTGTGGGTGTGTCTTGCTGAGTACGGTGGTTGTACTCAATCTTGCT[C/T]
ATTTTTTCCCCAACCTAGAAGAGGAGTTCCTGGAGGATGATGGCGTTGGTGTCTAGCTCGTGCCTGCCGTCAAGTGCCTGTGGTCGTCGCCCTAGTCTTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	70.80%	27.00%	2.14%	0.00%	NA
All Indica	2759	51.70%	45.00%	3.33%	0.00%	NA
All Japonica	1512	98.90%	1.00%	0.07%	0.00%	NA
Aus	269	98.90%	0.40%	0.74%	0.00%	NA
Indica I	595	16.80%	76.80%	6.39%	0.00%	NA
Indica II	465	35.70%	59.80%	4.52%	0.00%	NA
Indica III	913	83.50%	15.70%	0.88%	0.00%	NA
Indica Intermediate	786	50.60%	46.20%	3.18%	0.00%	NA
Temperate Japonica	767	98.30%	1.60%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	71.10%	22.20%	6.67%	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
vg0622322008	G -> A	LOC_Os06g37670.1	downstream_gene_variant ; 2991.0bp to feature; MODIFIER	silent_mutation	Average:64.297; most accessible tissue: Minghui63 flag leaf, score: 72.472	N	N	N	N
vg0622322008	G -> A	LOC_Os06g37670-LOC_Os06g37680	intergenic_region ; MODIFIER	silent_mutation	Average:64.297; most accessible tissue: Minghui63 flag leaf, score: 72.472	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0622322008	NA	8.15E-06	mr1006	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
vg0622322008	NA	8.61E-06	mr1007	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
vg0622322008	NA	2.51E-06	mr1037	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
vg0622322008	NA	4.18E-06	mr1052	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
vg0622322008	NA	3.73E-07	mr1078	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
vg0622322008	NA	6.09E-30	mr1237	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
vg0622322008	NA	1.37E-07	mr1237	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
vg0622322008	1.59E-06	1.21E-07	mr1887	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
vg0622322008	NA	2.92E-11	mr1067_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
vg0622322008	NA	1.24E-07	mr1078_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
vg0622322008	NA	1.28E-07	mr1100_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
vg0622322008	NA	3.22E-06	mr1133_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
vg0622322008	NA	1.40E-07	mr1212_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
vg0622322008	NA	1.01E-07	mr1526_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