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Detailed information for vg0907668817:

Variant ID: vg0907668817 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7668817
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, C: 0.08, others allele: 0.00, population size: 62. )

Flanking Sequence (100 bp) in Reference Genome:

ATAAGAGTTCGCTGTGTCGATTCCGCTCTCACGCGACTGATCTCGTCGCAGGCGTCCAACATCAGCTAACAGGATCATCAAGTGTTGCGTCGTCGTTCCC[C/G]
AATCCCGAGCCACATGCGAAGTCGATCTCAGACGGCACGATGACTACTATGTGTCTACGTCGAATGGATCGATATTCGTGTTTATATGCTTGGGAATTGA

Reverse complement sequence

TCAATTCCCAAGCATATAAACACGAATATCGATCCATTCGACGTAGACACATAGTAGTCATCGTGCCGTCTGAGATCGACTTCGCATGTGGCTCGGGATT[G/C]
GGGAACGACGACGCAACACTTGATGATCCTGTTAGCTGATGTTGGACGCCTGCGACGAGATCAGTCGCGTGAGAGCGGAATCGACACAGCGAACTCTTAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.10%	4.70%	6.05%	56.20%	NA
All Indica	2759	14.60%	0.40%	4.31%	80.72%	NA
All Japonica	1512	64.50%	13.60%	9.85%	12.04%	NA
Aus	269	16.00%	0.00%	3.35%	80.67%	NA
Indica I	595	9.70%	0.30%	8.57%	81.34%	NA
Indica II	465	6.50%	0.40%	4.73%	88.39%	NA
Indica III	913	21.50%	0.10%	1.10%	77.33%	NA
Indica Intermediate	786	15.10%	0.60%	4.58%	79.64%	NA
Temperate Japonica	767	40.20%	22.60%	16.04%	21.25%	NA
Tropical Japonica	504	94.80%	0.80%	2.98%	1.39%	NA
Japonica Intermediate	241	78.40%	12.00%	4.56%	4.98%	NA
VI/Aromatic	96	94.80%	0.00%	1.04%	4.17%	NA
Intermediate	90	55.60%	6.70%	8.89%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0907668817	C -> G	LOC_Os09g13290.1	downstream_gene_variant ; 4989.0bp to feature; MODIFIER	silent_mutation	Average:14.571; most accessible tissue: Callus, score: 84.58	N	N	N	N
vg0907668817	C -> G	LOC_Os09g13300.1	downstream_gene_variant ; 1886.0bp to feature; MODIFIER	silent_mutation	Average:14.571; most accessible tissue: Callus, score: 84.58	N	N	N	N
vg0907668817	C -> G	LOC_Os09g13290-LOC_Os09g13300	intergenic_region ; MODIFIER	silent_mutation	Average:14.571; most accessible tissue: Callus, score: 84.58	N	N	N	N
vg0907668817	C -> DEL	N	N	silent_mutation	Average:14.571; most accessible tissue: Callus, score: 84.58	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907668817	NA	1.68E-06	mr1034	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
vg0907668817	4.78E-08	NA	mr1057	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
vg0907668817	7.20E-06	7.18E-06	mr1494	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