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Detailed information for vg0909780560:

Variant ID: vg0909780560 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9780560
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, G: 0.05, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

TATCCTGTTTAGAGAGTCTTGAGATGGCAGGATGCTGTAGTCTTCAGAGATTACCAGAATCGTTTGGTGGCCTCTCTAAGCTCTGTTCTTTAAGCTTAGC[A/G]
AGTTGTTCTAGCCTTCAACGATTGCCAGATTATATTGGTGAGTTGTGTAGTTTAGAGTACTTGAACATTTCACATGCTCACCTTGAGCTACCGGATTCAC

Reverse complement sequence

GTGAATCCGGTAGCTCAAGGTGAGCATGTGAAATGTTCAAGTACTCTAAACTACACAACTCACCAATATAATCTGGCAATCGTTGAAGGCTAGAACAACT[T/C]
GCTAAGCTTAAAGAACAGAGCTTAGAGAGGCCACCAAACGATTCTGGTAATCTCTGAAGACTACAGCATCCTGCCATCTCAAGACTCTCTAAACAGGATA

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	84.30%	15.40%	0.00%	0.32%	NA
All Indica	2759	78.10%	21.50%	0.00%	0.47%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	73.60%	26.40%	0.00%	0.00%	NA
Indica I	595	89.10%	10.80%	0.00%	0.17%	NA
Indica II	465	79.60%	18.70%	0.00%	1.72%	NA
Indica III	913	70.30%	29.70%	0.00%	0.00%	NA
Indica Intermediate	786	77.90%	21.60%	0.00%	0.51%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	54.20%	45.80%	0.00%	0.00%	NA
Intermediate	90	85.60%	12.20%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909780560	A -> G	LOC_Os09g16000.1	synonymous_variant ; p.Ala698Ala; LOW	synonymous_codon	Average:63.296; most accessible tissue: Callus, score: 88.062	N	N	N	N
vg0909780560	A -> DEL	LOC_Os09g16000.1	N	frameshift_variant	Average:63.296; most accessible tissue: Callus, score: 88.062	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909780560	5.32E-07	NA	mr1386_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
vg0909780560	NA	9.06E-07	mr1386_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