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Detailed information for vg0909065986:

Variant ID: vg0909065986 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9065986
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.06, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

GTATGTTCTACCGCTGCTAGACTACAAGACAAGATTCTCGCTGTGGCAAGTCAAGATGCGGGCTGTTCTGGCGCAAACTTCGGATCTTGATGAGGCGCTG[A/G]
AAAGCTTCGGGAAGAAGAAATCGACTGAATGGACCGCTGAGGAGAAGCGGAAAGATCGTAAGGCTCTGTCACTGATCCAACTTCATCTATCTAATGATAT

Reverse complement sequence

ATATCATTAGATAGATGAAGTTGGATCAGTGACAGAGCCTTACGATCTTTCCGCTTCTCCTCAGCGGTCCATTCAGTCGATTTCTTCTTCCCGAAGCTTT[T/C]
CAGCGCCTCATCAAGATCCGAAGTTTGCGCCAGAACAGCCCGCATCTTGACTTGCCACAGCGAGAATCTTGTCTTGTAGTCTAGCAGCGGTAGAACATAC

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	50.70%	34.70%	10.66%	3.89%	NA
All Indica	2759	67.10%	9.50%	16.85%	6.56%	NA
All Japonica	1512	14.10%	85.70%	0.20%	0.00%	NA
Aus	269	89.20%	3.70%	7.06%	0.00%	NA
Indica I	595	74.30%	6.40%	16.47%	2.86%	NA
Indica II	465	68.60%	5.40%	22.80%	3.23%	NA
Indica III	913	59.70%	14.30%	13.69%	12.27%	NA
Indica Intermediate	786	69.30%	8.70%	17.30%	4.71%	NA
Temperate Japonica	767	13.40%	86.20%	0.39%	0.00%	NA
Tropical Japonica	504	7.50%	92.50%	0.00%	0.00%	NA
Japonica Intermediate	241	29.90%	70.10%	0.00%	0.00%	NA
VI/Aromatic	96	62.50%	21.90%	14.58%	1.04%	NA
Intermediate	90	37.80%	56.70%	3.33%	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
vg0909065986	A -> G	LOC_Os09g15030.1	missense_variant ; p.Lys39Glu; MODERATE	nonsynonymous_codon ; K39E	Average:19.705; most accessible tissue: Zhenshan97 flag leaf, score: 28.494	unknown	unknown	TOLERATED	1.00
vg0909065986	A -> DEL	LOC_Os09g15030.1	N	frameshift_variant	Average:19.705; most accessible tissue: Zhenshan97 flag leaf, score: 28.494	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909065986	NA	9.80E-06	mr1944	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
vg0909065986	NA	5.25E-09	mr1299_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
vg0909065986	NA	6.21E-08	mr1700_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
vg0909065986	NA	6.77E-09	mr1727_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
vg0909065986	NA	1.34E-11	mr1756_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
vg0909065986	NA	5.10E-07	mr1840_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
vg0909065986	NA	5.85E-06	mr1856_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