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Detailed information for vg1215321457:

Variant ID: vg1215321457 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15321457
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, T: 0.19, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

GATTGAGATGTGTAATTTTGTGATTCATTGCATGTATATGAGATGTATAATCTGTGATGTATTTAATTTGTGTGTATTTTTGAGGATTTGTGATGTATTT[G/T]
ATTTGAGTGTATTTTTTTAGGATTTGTGATGTATTTGATTTATGTTTGTAAGTAACTTAAGATTTGGGATGTTACTTTGAATTGGGGTTGTGGGGATTGA

Reverse complement sequence

TCAATCCCCACAACCCCAATTCAAAGTAACATCCCAAATCTTAAGTTACTTACAAACATAAATCAAATACATCACAAATCCTAAAAAAATACACTCAAAT[C/A]
AAATACATCACAAATCCTCAAAAATACACACAAATTAAATACATCACAGATTATACATCTCATATACATGCAATGAATCACAAAATTACACATCTCAATC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.90%	37.90%	0.15%	0.00%	NA
All Indica	2759	71.30%	28.50%	0.22%	0.00%	NA
All Japonica	1512	37.20%	62.80%	0.00%	0.00%	NA
Aus	269	93.70%	6.30%	0.00%	0.00%	NA
Indica I	595	95.00%	5.00%	0.00%	0.00%	NA
Indica II	465	42.40%	57.20%	0.43%	0.00%	NA
Indica III	913	77.30%	22.50%	0.22%	0.00%	NA
Indica Intermediate	786	63.50%	36.30%	0.25%	0.00%	NA
Temperate Japonica	767	8.60%	91.40%	0.00%	0.00%	NA
Tropical Japonica	504	80.40%	19.60%	0.00%	0.00%	NA
Japonica Intermediate	241	38.20%	61.80%	0.00%	0.00%	NA
VI/Aromatic	96	88.50%	11.50%	0.00%	0.00%	NA
Intermediate	90	65.60%	33.30%	1.11%	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
vg1215321457	G -> T	LOC_Os12g26270.1	downstream_gene_variant ; 2526.0bp to feature; MODIFIER	silent_mutation	Average:30.015; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg1215321457	G -> T	LOC_Os12g26260-LOC_Os12g26270	intergenic_region ; MODIFIER	silent_mutation	Average:30.015; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215321457	NA	2.33E-07	mr1022	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
vg1215321457	NA	1.00E-11	mr1132	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
vg1215321457	NA	9.66E-11	mr1178	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
vg1215321457	1.92E-06	1.92E-06	mr1266	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
vg1215321457	NA	7.23E-12	mr1390	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
vg1215321457	NA	2.03E-11	mr1490	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
vg1215321457	NA	1.31E-08	mr1889	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
vg1215321457	NA	8.53E-08	mr1942	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
vg1215321457	NA	8.53E-12	mr1022_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
vg1215321457	NA	1.89E-18	mr1023_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
vg1215321457	NA	5.89E-16	mr1079_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
vg1215321457	NA	1.65E-13	mr1178_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
vg1215321457	NA	1.89E-15	mr1489_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
vg1215321457	NA	2.74E-10	mr1942_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