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Detailed information for vg0810788386:

Variant ID: vg0810788386 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 10788386
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

GGGTTAGTGATGCGACATAGCCATCAAGCCATGTCTACCACATCACCATAAAACAAAGCTGTAAAATAACCCTGTCCAATCCTCACGTTCGGCTGATCTC[G/A]
TAACAGCTACTAATAAATAATTTATTATTTCCTCATTGGAAATGGTTTAGATTAAATCAAATCTATGTTACTAAAAATTAGCTCTTATGTAGACAAAAAT

Reverse complement sequence

ATTTTTGTCTACATAAGAGCTAATTTTTAGTAACATAGATTTGATTTAATCTAAACCATTTCCAATGAGGAAATAATAAATTATTTATTAGTAGCTGTTA[C/T]
GAGATCAGCCGAACGTGAGGATTGGACAGGGTTATTTTACAGCTTTGTTTTATGGTGATGTGGTAGACATGGCTTGATGGCTATGTCGCATCACTAACCC

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	82.20%	1.40%	0.38%	16.00%	NA
All Indica	2759	96.30%	0.20%	0.07%	3.37%	NA
All Japonica	1512	58.10%	3.90%	0.73%	37.24%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.00%	0.00%	0.65%	NA
Indica III	913	90.70%	0.40%	0.00%	8.87%	NA
Indica Intermediate	786	98.30%	0.30%	0.25%	1.15%	NA
Temperate Japonica	767	90.50%	7.30%	0.13%	2.09%	NA
Tropical Japonica	504	15.90%	0.00%	1.59%	82.54%	NA
Japonica Intermediate	241	43.60%	1.20%	0.83%	54.36%	NA
VI/Aromatic	96	14.60%	0.00%	3.12%	82.29%	NA
Intermediate	90	74.40%	0.00%	2.22%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0810788386	G -> A	LOC_Os08g17640-LOC_Os08g17650	intergenic_region ; MODIFIER	silent_mutation	Average:54.805; most accessible tissue: Minghui63 flower, score: 70.218	N	N	N	N
vg0810788386	G -> DEL	N	N	silent_mutation	Average:54.805; most accessible tissue: Minghui63 flower, score: 70.218	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0810788386	NA	9.57E-06	mr1045_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
vg0810788386	NA	1.86E-06	mr1129_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
vg0810788386	NA	9.48E-06	mr1200_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
vg0810788386	1.33E-07	7.51E-08	mr1255_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
vg0810788386	NA	6.57E-06	mr1405_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
vg0810788386	NA	1.10E-06	mr1458_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
vg0810788386	NA	9.05E-06	mr1874_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