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Detailed information for vg1214549363:

Variant ID: vg1214549363 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14549363
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TCGGCCGAAATTTTTGAATTTTTTCATGAATTTGGATAATATTTATTCAAATTCAACTAAATTTTGTTTAAAATTTCAAAAATTTCGGACCAAAATTTCC[G/A]
AAATTTCGGGATTTCGGTGACCCCCAATCAAAAACCCTAAACCAATACAGTGAACCCTGCTTACAACTTTTAAGTTTCCTTTTTCTATTAACTATAATAT

Reverse complement sequence

ATATTATAGTTAATAGAAAAAGGAAACTTAAAAGTTGTAAGCAGGGTTCACTGTATTGGTTTAGGGTTTTTGATTGGGGGTCACCGAAATCCCGAAATTT[C/T]
GGAAATTTTGGTCCGAAATTTTTGAAATTTTAAACAAAATTTAGTTGAATTTGAATAAATATTATCCAAATTCATGAAAAAATTCAAAAATTTCGGCCGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.60%	48.20%	1.18%	0.00%	NA
All Indica	2759	70.70%	28.80%	0.51%	0.00%	NA
All Japonica	1512	25.70%	71.90%	2.38%	0.00%	NA
Aus	269	3.70%	96.30%	0.00%	0.00%	NA
Indica I	595	65.40%	34.30%	0.34%	0.00%	NA
Indica II	465	70.10%	29.00%	0.86%	0.00%	NA
Indica III	913	76.30%	23.20%	0.44%	0.00%	NA
Indica Intermediate	786	68.60%	30.90%	0.51%	0.00%	NA
Temperate Japonica	767	21.90%	73.80%	4.30%	0.00%	NA
Tropical Japonica	504	30.80%	68.80%	0.40%	0.00%	NA
Japonica Intermediate	241	27.40%	72.20%	0.41%	0.00%	NA
VI/Aromatic	96	10.40%	89.60%	0.00%	0.00%	NA
Intermediate	90	35.60%	57.80%	6.67%	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
vg1214549363	G -> A	LOC_Os12g25280-LOC_Os12g25290	intergenic_region ; MODIFIER	silent_mutation	Average:39.625; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214549363	NA	8.69E-06	mr1817	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
vg1214549363	4.46E-06	4.45E-06	mr1299_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
vg1214549363	NA	2.98E-06	mr1422_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
vg1214549363	7.86E-06	7.86E-06	mr1727_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
vg1214549363	3.35E-06	9.34E-07	mr1900_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