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Detailed information for vg0708802081:

Variant ID: vg0708802081 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 8802081
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

CGAATGGTCTGCCAAAATTGGTTCCTCACCTTGCGCAGTTGCAGCCTCCTTTTGCAGTTTTTTTTTGCTGCAAATTCGGGTTCGTTTTTGTTTTGGAAAC[G/A]
TTCCGAAAATCCGGTGCGTGAAAACGGCGTGGAGTCCGGATAAGTTACGCACGACTTATCCGGTTCGGTTACGTAGAGTGGAGATCGTGCGGGCGCTCTG

Reverse complement sequence

CAGAGCGCCCGCACGATCTCCACTCTACGTAACCGAACCGGATAAGTCGTGCGTAACTTATCCGGACTCCACGCCGTTTTCACGCACCGGATTTTCGGAA[C/T]
GTTTCCAAAACAAAAACGAACCCGAATTTGCAGCAAAAAAAAACTGCAAAAGGAGGCTGCAACTGCGCAAGGTGAGGAACCAATTTTGGCAGACCATTCG

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	59.10%	40.60%	0.25%	0.00%	NA
All Indica	2759	34.40%	65.30%	0.29%	0.00%	NA
All Japonica	1512	94.20%	5.50%	0.26%	0.00%	NA
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	78.70%	21.00%	0.34%	0.00%	NA
Indica II	465	18.70%	81.30%	0.00%	0.00%	NA
Indica III	913	8.90%	91.00%	0.11%	0.00%	NA
Indica Intermediate	786	39.80%	59.50%	0.64%	0.00%	NA
Temperate Japonica	767	96.70%	2.70%	0.52%	0.00%	NA
Tropical Japonica	504	88.70%	11.30%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	68.90%	31.10%	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
vg0708802081	G -> A	LOC_Os07g15260.1	downstream_gene_variant ; 917.0bp to feature; MODIFIER	silent_mutation	Average:45.243; most accessible tissue: Zhenshan97 flag leaf, score: 73.119	N	N	N	N
vg0708802081	G -> A	LOC_Os07g15260-LOC_Os07g15270	intergenic_region ; MODIFIER	silent_mutation	Average:45.243; most accessible tissue: Zhenshan97 flag leaf, score: 73.119	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0708802081	NA	1.14E-17	mr1170	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
vg0708802081	NA	1.19E-07	mr1170	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
vg0708802081	NA	1.06E-10	mr1565	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
vg0708802081	NA	1.11E-08	mr1565	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
vg0708802081	NA	2.57E-06	mr1629	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
vg0708802081	NA	9.15E-12	mr1170_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
vg0708802081	NA	3.25E-08	mr1170_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
vg0708802081	NA	3.37E-08	mr1629_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
vg0708802081	NA	5.77E-06	mr1968_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