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Detailed information for vg1218097299:

Variant ID: vg1218097299 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18097299
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, T: 0.02, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

TAGCCTGTTGCCCAAATGTGCACGTCACATAGGTGGTGTTTGGATCAGGGACTTAACTTTAGTCTTTATATTTATATACTAATTTAAAGTATTAAATATA[G/T]
ACTACTTACAAAACTAATTACATAAATGAAAGCTAATTCATGAGACAAATTTTTAAAACCTAATTAATCCATAATTAGAAAATGTTTACTCTAGCATCAC

Reverse complement sequence

GTGATGCTAGAGTAAACATTTTCTAATTATGGATTAATTAGGTTTTAAAAATTTGTCTCATGAATTAGCTTTCATTTATGTAATTAGTTTTGTAAGTAGT[C/A]
TATATTTAATACTTTAAATTAGTATATAAATATAAAGACTAAAGTTAAGTCCCTGATCCAAACACCACCTATGTGACGTGCACATTTGGGCAACAGGCTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.60%	26.30%	0.11%	0.00%	NA
All Indica	2759	66.20%	33.70%	0.11%	0.00%	NA
All Japonica	1512	94.80%	5.20%	0.00%	0.00%	NA
Aus	269	29.70%	70.30%	0.00%	0.00%	NA
Indica I	595	98.00%	1.80%	0.17%	0.00%	NA
Indica II	465	56.80%	43.20%	0.00%	0.00%	NA
Indica III	913	49.40%	50.50%	0.11%	0.00%	NA
Indica Intermediate	786	67.20%	32.70%	0.13%	0.00%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	0.00%	NA
Tropical Japonica	504	95.80%	4.20%	0.00%	0.00%	NA
Japonica Intermediate	241	78.00%	22.00%	0.00%	0.00%	NA
VI/Aromatic	96	70.80%	28.10%	1.04%	0.00%	NA
Intermediate	90	77.80%	21.10%	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
vg1218097299	G -> T	LOC_Os12g30150.1	upstream_gene_variant ; 1376.0bp to feature; MODIFIER	silent_mutation	Average:43.92; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg1218097299	G -> T	LOC_Os12g30140-LOC_Os12g30150	intergenic_region ; MODIFIER	silent_mutation	Average:43.92; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218097299	NA	3.18E-15	mr1232	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
vg1218097299	NA	6.53E-06	mr1232	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
vg1218097299	NA	1.63E-09	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
vg1218097299	NA	1.39E-09	mr1232_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
vg1218097299	NA	7.82E-06	mr1232_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
vg1218097299	NA	5.57E-08	mr1557_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