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Detailed information for vg1219857888:

Variant ID: vg1219857888 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19857888
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

GCAGTGGGTGGATCTGGACTAGGGGCACGAGATATCTAGGTGTGTTATTTTCGTGTGCGGGTCACTTAACAGGCCCGTACACGAAAATAGGCTTATTTTC[G/A]
CGTGTGGGCCTGTTAAGTGACCTGCACACGAAAATTGATTTTCCTGTGCGGGCGATGGTCTGGCGCCGGTCCCTCCCATTTTCCTGTGCGGTTCCACTTA

Reverse complement sequence

TAAGTGGAACCGCACAGGAAAATGGGAGGGACCGGCGCCAGACCATCGCCCGCACAGGAAAATCAATTTTCGTGTGCAGGTCACTTAACAGGCCCACACG[C/T]
GAAAATAAGCCTATTTTCGTGTACGGGCCTGTTAAGTGACCCGCACACGAAAATAACACACCTAGATATCTCGTGCCCCTAGTCCAGATCCACCCACTGC

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	54.30%	44.90%	0.87%	0.00%	NA
All Indica	2759	37.00%	62.50%	0.47%	0.00%	NA
All Japonica	1512	90.80%	7.50%	1.65%	0.00%	NA
Aus	269	7.40%	92.20%	0.37%	0.00%	NA
Indica I	595	29.40%	69.70%	0.84%	0.00%	NA
Indica II	465	40.60%	59.10%	0.22%	0.00%	NA
Indica III	913	36.30%	63.30%	0.44%	0.00%	NA
Indica Intermediate	786	41.60%	58.00%	0.38%	0.00%	NA
Temperate Japonica	767	94.00%	5.10%	0.91%	0.00%	NA
Tropical Japonica	504	87.50%	10.10%	2.38%	0.00%	NA
Japonica Intermediate	241	87.60%	10.00%	2.49%	0.00%	NA
VI/Aromatic	96	87.50%	12.50%	0.00%	0.00%	NA
Intermediate	90	72.20%	25.60%	2.22%	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
vg1219857888	G -> A	LOC_Os12g32850-LOC_Os12g32870	intergenic_region ; MODIFIER	silent_mutation	Average:66.613; most accessible tissue: Zhenshan97 young leaf, score: 87.299	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219857888	NA	3.48E-07	mr1458	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
vg1219857888	1.64E-06	NA	mr1334_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
vg1219857888	NA	3.03E-08	mr1458_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