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Detailed information for vg0407565317:

Variant ID: vg0407565317 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 7565317
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.89, G: 0.11, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

ATAGTTGCCATGTCCCTATAATCATGATTACCATTATTAATTTACAGAGGTAAATTAATAAAAAACATGATATTGCAGTTGTAATCTCAATGCGAAATGT[A/G]
AGACTTCATATTTTGTAATGTTTCGAAAAGATGTAGGTAATAGACCTGACAATTTGATTTAGAATTCGAATTTAGGTGGCACAAAAGTGGATAATCTCCA

Reverse complement sequence

TGGAGATTATCCACTTTTGTGCCACCTAAATTCGAATTCTAAATCAAATTGTCAGGTCTATTACCTACATCTTTTCGAAACATTACAAAATATGAAGTCT[T/C]
ACATTTCGCATTGAGATTACAACTGCAATATCATGTTTTTTATTAATTTACCTCTGTAAATTAATAATGGTAATCATGATTATAGGGACATGGCAACTAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	30.60%	12.30%	3.39%	53.70%	NA
All Indica	2759	13.00%	1.90%	5.04%	80.03%	NA
All Japonica	1512	65.20%	33.40%	0.20%	1.19%	NA
Aus	269	5.60%	0.40%	3.72%	90.33%	NA
Indica I	595	11.60%	0.30%	8.07%	80.00%	NA
Indica II	465	26.00%	2.60%	4.09%	67.31%	NA
Indica III	913	9.40%	2.70%	3.61%	84.23%	NA
Indica Intermediate	786	10.70%	1.70%	4.96%	82.70%	NA
Temperate Japonica	767	96.20%	3.40%	0.00%	0.39%	NA
Tropical Japonica	504	14.90%	82.30%	0.60%	2.18%	NA
Japonica Intermediate	241	71.80%	26.60%	0.00%	1.66%	NA
VI/Aromatic	96	47.90%	6.20%	8.33%	37.50%	NA
Intermediate	90	44.40%	18.90%	0.00%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0407565317	A -> DEL	N	N	silent_mutation	Average:11.864; most accessible tissue: Callus, score: 29.229	N	N	N	N
vg0407565317	A -> G	LOC_Os04g13550.1	intron_variant ; MODIFIER	silent_mutation	Average:11.864; most accessible tissue: Callus, score: 29.229	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0407565317	2.54E-06	NA	mr1071	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
vg0407565317	3.66E-06	NA	mr1140	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
vg0407565317	NA	9.24E-07	mr1220	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
vg0407565317	NA	2.90E-22	mr1301	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
vg0407565317	NA	3.35E-15	mr1301	Jap_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
vg0407565317	NA	5.77E-16	mr1410	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
vg0407565317	NA	3.21E-11	mr1410	Jap_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
vg0407565317	NA	2.68E-14	mr1449	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
vg0407565317	NA	9.31E-06	mr1502	Jap_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
vg0407565317	NA	1.26E-08	mr1648	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
vg0407565317	NA	1.76E-28	mr1699	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
vg0407565317	NA	6.12E-07	mr1739	Jap_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
vg0407565317	NA	9.47E-07	mr1993	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
vg0407565317	NA	7.45E-08	mr1993	Jap_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
vg0407565317	1.72E-10	NA	mr1071_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
vg0407565317	4.53E-11	NA	mr1080_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
vg0407565317	8.49E-09	NA	mr1100_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
vg0407565317	4.49E-13	NA	mr1203_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
vg0407565317	1.52E-06	2.29E-25	mr1301_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
vg0407565317	NA	1.24E-18	mr1301_2	Jap_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
vg0407565317	NA	7.89E-17	mr1410_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
vg0407565317	NA	4.90E-06	mr1510_2	Jap_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
vg0407565317	4.43E-14	NA	mr1613_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
vg0407565317	3.46E-11	NA	mr1619_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
vg0407565317	7.12E-07	NA	mr1962_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
vg0407565317	NA	6.09E-12	mr1993_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
vg0407565317	NA	2.90E-12	mr1993_2	Jap_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