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Detailed information for vg0805790576:

Variant ID: vg0805790576 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 5790576
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.51, A: 0.49, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

TTTCGCTCTTCCGTTCCACGAGATAGCGCACGGTCTTGCACTTTCCCAGTGCGATACCGCCCACGATGTCACGCCCACATCATTTTTGTGCAACGGTTAT[G/A]
CGAGATCGACGATATATTTGTGCAAAAAAAATTTGCATCCTAAATATTACTGAAAAAAAATTGAATGTACGGTAGATTTTTAGATTTAATTAAGAGATAC

Reverse complement sequence

GTATCTCTTAATTAAATCTAAAAATCTACCGTACATTCAATTTTTTTTCAGTAATATTTAGGATGCAAATTTTTTTTGCACAAATATATCGTCGATCTCG[C/T]
ATAACCGTTGCACAAAAATGATGTGGGCGTGACATCGTGGGCGGTATCGCACTGGGAAAGTGCAAGACCGTGCGCTATCTCGTGGAACGGAAGAGCGAAA

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	79.10%	20.50%	0.13%	0.28%	NA
All Indica	2759	68.80%	30.60%	0.22%	0.43%	NA
All Japonica	1512	93.30%	6.60%	0.00%	0.07%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	54.50%	44.70%	0.17%	0.67%	NA
Indica II	465	54.40%	44.70%	0.43%	0.43%	NA
Indica III	913	88.50%	11.30%	0.22%	0.00%	NA
Indica Intermediate	786	65.30%	33.80%	0.13%	0.76%	NA
Temperate Japonica	767	96.60%	3.30%	0.00%	0.13%	NA
Tropical Japonica	504	86.90%	13.10%	0.00%	0.00%	NA
Japonica Intermediate	241	96.30%	3.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	76.70%	23.30%	0.00%	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
vg0805790576	G -> A	LOC_Os08g10010.1	upstream_gene_variant ; 1436.0bp to feature; MODIFIER	silent_mutation	Average:48.24; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0805790576	G -> A	LOC_Os08g10010-LOC_Os08g10020	intergenic_region ; MODIFIER	silent_mutation	Average:48.24; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0805790576	G -> DEL	N	N	silent_mutation	Average:48.24; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0805790576	NA	2.08E-08	mr1136	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
vg0805790576	NA	2.32E-06	mr1471	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
vg0805790576	NA	2.14E-06	mr1484	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
vg0805790576	NA	1.17E-06	mr1728	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
vg0805790576	NA	3.13E-07	mr1850	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
vg0805790576	2.08E-06	2.08E-06	mr1945	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