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Detailed information for vg0909816527:

Variant ID: vg0909816527 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9816527
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.56, G: 0.44, others allele: 0.00, population size: 62. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGGAGTATTTTTTACTTGAAAAGCCGGTGCTTGATTTTTAAGTCTTTGGATGAAATTGGCCAAATCACAGACTAGGGGCGGTCTGACTGGCATTGCAC[A/G]
GCCGGTCTGACCGGTGATGACCGGCGGTCTGACCGGCTCTGCATGGCCGGTCCGACCGGATAGACAGGGAGGTCTGACCGGCATTGTGCGTCCGGTCTGA

Reverse complement sequence

TCAGACCGGACGCACAATGCCGGTCAGACCTCCCTGTCTATCCGGTCGGACCGGCCATGCAGAGCCGGTCAGACCGCCGGTCATCACCGGTCAGACCGGC[T/C]
GTGCAATGCCAGTCAGACCGCCCCTAGTCTGTGATTTGGCCAATTTCATCCAAAGACTTAAAAATCAAGCACCGGCTTTTCAAGTAAAAAATACTCCTTT

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	45.20%	14.10%	7.58%	33.14%	NA
All Indica	2759	27.10%	20.00%	10.33%	42.59%	NA
All Japonica	1512	81.20%	0.50%	0.26%	18.12%	NA
Aus	269	7.40%	36.10%	24.16%	32.34%	NA
Indica I	595	19.80%	3.20%	10.08%	66.89%	NA
Indica II	465	22.40%	14.40%	7.74%	55.48%	NA
Indica III	913	33.50%	37.10%	10.95%	18.40%	NA
Indica Intermediate	786	28.00%	16.00%	11.32%	44.66%	NA
Temperate Japonica	767	80.80%	0.00%	0.26%	18.90%	NA
Tropical Japonica	504	78.60%	1.20%	0.40%	19.84%	NA
Japonica Intermediate	241	87.60%	0.40%	0.00%	12.03%	NA
VI/Aromatic	96	88.50%	2.10%	1.04%	8.33%	NA
Intermediate	90	61.10%	11.10%	3.33%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909816527	A -> G	LOC_Os09g16080.1	intron_variant ; MODIFIER	silent_mutation	Average:30.579; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0909816527	A -> DEL	N	N	silent_mutation	Average:30.579; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909816527	NA	2.58E-12	mr1170	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
vg0909816527	NA	2.24E-10	mr1630	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
vg0909816527	5.22E-07	5.22E-07	mr1869	Ind_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