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Detailed information for vg1208985464:

Variant ID: vg1208985464 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8985464
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.82, A: 0.17, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTTAGGTGTTCAGAAGATCCATTCATGTGAAAATTATTGCATACTGTACAGCAAGAAATTCGCGGATTTAGACTCTTGCCCAACATGTGGGACGAGTC[G/A]
GTACAAGACGGGTAACGGAGCCTCCGATGGAGAGGTGGTCGACAAAGATGATGCACCGGTGGATGAGAAAAAAAAGATTCCTAGGATGGTGGTGTGGTAC

Reverse complement sequence

GTACCACACCACCATCCTAGGAATCTTTTTTTTCTCATCCACCGGTGCATCATCTTTGTCGACCACCTCTCCATCGGAGGCTCCGTTACCCGTCTTGTAC[C/T]
GACTCGTCCCACATGTTGGGCAAGAGTCTAAATCCGCGAATTTCTTGCTGTACAGTATGCAATAATTTTCACATGAATGGATCTTCTGAACACCTAAAGA

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	58.00%	30.60%	1.57%	9.86%	NA
All Indica	2759	33.00%	48.30%	2.50%	16.20%	NA
All Japonica	1512	95.10%	4.00%	0.07%	0.79%	NA
Aus	269	97.00%	1.10%	1.12%	0.74%	NA
Indica I	595	51.90%	30.40%	2.02%	15.63%	NA
Indica II	465	22.80%	49.20%	0.43%	27.53%	NA
Indica III	913	24.30%	60.40%	3.07%	12.27%	NA
Indica Intermediate	786	34.90%	47.20%	3.44%	14.50%	NA
Temperate Japonica	767	93.60%	5.60%	0.00%	0.78%	NA
Tropical Japonica	504	95.80%	3.40%	0.20%	0.60%	NA
Japonica Intermediate	241	98.30%	0.40%	0.00%	1.24%	NA
VI/Aromatic	96	62.50%	35.40%	0.00%	2.08%	NA
Intermediate	90	76.70%	18.90%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208985464	G -> DEL	N	N	silent_mutation	Average:32.748; most accessible tissue: Callus, score: 65.108	N	N	N	N
vg1208985464	G -> A	LOC_Os12g15730.1	upstream_gene_variant ; 647.0bp to feature; MODIFIER	silent_mutation	Average:32.748; most accessible tissue: Callus, score: 65.108	N	N	N	N
vg1208985464	G -> A	LOC_Os12g15740.1	downstream_gene_variant ; 2854.0bp to feature; MODIFIER	silent_mutation	Average:32.748; most accessible tissue: Callus, score: 65.108	N	N	N	N
vg1208985464	G -> A	LOC_Os12g15700-LOC_Os12g15730	intergenic_region ; MODIFIER	silent_mutation	Average:32.748; most accessible tissue: Callus, score: 65.108	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208985464	5.91E-07	3.35E-11	mr1425	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
vg1208985464	5.12E-07	6.06E-11	mr1425	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
vg1208985464	NA	4.01E-07	mr1425_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