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Detailed information for vg1227115867:

Variant ID: vg1227115867 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 27115867
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

CTAAAAGTAATGAATTTTTAGGCCAAATGTTTATAATCATGAAATTTTGAGCAAAAGTCTAATAATCACGCTCTTTTATGACTAAGGCTAATCCTTTATG[G/A]
GTGTTTTTTAGCCAAAGCCTAAAATCAAGAATTTTTAGGCCAAAGGTTTAAAATCACGAAATTTTGGATAAAGTAATATTCAAACCTTTTTTTAGCCCAA

Reverse complement sequence

TTGGGCTAAAAAAAGGTTTGAATATTACTTTATCCAAAATTTCGTGATTTTAAACCTTTGGCCTAAAAATTCTTGATTTTAGGCTTTGGCTAAAAAACAC[C/T]
CATAAAGGATTAGCCTTAGTCATAAAAGAGCGTGATTATTAGACTTTTGCTCAAAATTTCATGATTATAAACATTTGGCCTAAAAATTCATTACTTTTAG

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	55.00%	44.70%	0.28%	0.00%	NA
All Indica	2759	74.70%	25.10%	0.22%	0.00%	NA
All Japonica	1512	13.00%	86.90%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	21.30%	78.30%	0.34%	0.00%	NA
Indica II	465	88.60%	10.80%	0.65%	0.00%	NA
Indica III	913	95.00%	5.00%	0.00%	0.00%	NA
Indica Intermediate	786	83.30%	16.50%	0.13%	0.00%	NA
Temperate Japonica	767	22.90%	76.90%	0.13%	0.00%	NA
Tropical Japonica	504	2.00%	97.80%	0.20%	0.00%	NA
Japonica Intermediate	241	4.10%	95.90%	0.00%	0.00%	NA
VI/Aromatic	96	28.10%	69.80%	2.08%	0.00%	NA
Intermediate	90	51.10%	45.60%	3.33%	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
vg1227115867	G -> A	LOC_Os12g43640.1	downstream_gene_variant ; 3324.0bp to feature; MODIFIER	silent_mutation	Average:27.694; most accessible tissue: Callus, score: 58.716	N	N	N	N
vg1227115867	G -> A	LOC_Os12g43640-LOC_Os12g43660	intergenic_region ; MODIFIER	silent_mutation	Average:27.694; most accessible tissue: Callus, score: 58.716	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1227115867	NA	5.35E-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
vg1227115867	NA	3.88E-06	mr1586	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
vg1227115867	NA	3.65E-07	mr1659	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
vg1227115867	1.89E-06	1.89E-06	mr1074_2	Jap_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
vg1227115867	NA	6.96E-06	mr1128_2	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
vg1227115867	NA	1.93E-13	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
vg1227115867	NA	2.77E-06	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
vg1227115867	NA	4.20E-06	mr1184_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
vg1227115867	8.08E-06	8.08E-06	mr1256_2	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