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Detailed information for vg1206394265:

Variant ID: vg1206394265 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6394265
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

GCTGTCCTGTCCCTCTGCGCACCGGCGGCGCCGCTGCCCCCTCTCCCTCGATGCGCTAGAGCCGGCGTCGCTGCCCCCTCCCTCCGCCATCGTTCACGCC[G/A]
AGAGAGAAGAGAGTGAGAGAAAGATAATGATAAGAGATTGAAGGCAGGGAGGTAGCAGGTAGGAGGTGGATAAGATTGAAGGAAGGGTATTTTGGTCAAA

Reverse complement sequence

TTTGACCAAAATACCCTTCCTTCAATCTTATCCACCTCCTACCTGCTACCTCCCTGCCTTCAATCTCTTATCATTATCTTTCTCTCACTCTCTTCTCTCT[C/T]
GGCGTGAACGATGGCGGAGGGAGGGGGCAGCGACGCCGGCTCTAGCGCATCGAGGGAGAGGGGGCAGCGGCGCCGCCGGTGCGCAGAGGGACAGGACAGC

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	24.60%	15.70%	0.21%	59.44%	NA
All Indica	2759	35.30%	3.40%	0.04%	61.25%	NA
All Japonica	1512	5.70%	38.00%	0.46%	55.82%	NA
Aus	269	3.00%	17.10%	0.37%	79.55%	NA
Indica I	595	85.70%	6.10%	0.00%	8.24%	NA
Indica II	465	18.70%	2.40%	0.00%	78.92%	NA
Indica III	913	10.80%	2.00%	0.00%	87.19%	NA
Indica Intermediate	786	35.40%	3.70%	0.13%	60.81%	NA
Temperate Japonica	767	9.80%	44.70%	0.26%	45.24%	NA
Tropical Japonica	504	1.00%	22.00%	0.60%	76.39%	NA
Japonica Intermediate	241	2.50%	50.20%	0.83%	46.47%	NA
VI/Aromatic	96	68.80%	10.40%	0.00%	20.83%	NA
Intermediate	90	32.20%	21.10%	1.11%	45.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1206394265	G -> DEL	N	N	silent_mutation	Average:74.884; most accessible tissue: Callus, score: 96.462	N	N	N	N
vg1206394265	G -> A	LOC_Os12g11780.1	upstream_gene_variant ; 2321.0bp to feature; MODIFIER	silent_mutation	Average:74.884; most accessible tissue: Callus, score: 96.462	N	N	N	N
vg1206394265	G -> A	LOC_Os12g11790.1	upstream_gene_variant ; 11.0bp to feature; MODIFIER	silent_mutation	Average:74.884; most accessible tissue: Callus, score: 96.462	N	N	N	N
vg1206394265	G -> A	LOC_Os12g11790-LOC_Os12g11800	intergenic_region ; MODIFIER	silent_mutation	Average:74.884; most accessible tissue: Callus, score: 96.462	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206394265	NA	1.05E-06	mr1045_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
vg1206394265	5.27E-06	NA	mr1050_2	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
vg1206394265	1.32E-06	2.33E-08	mr1691_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
vg1206394265	6.97E-07	NA	mr1757_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
vg1206394265	6.24E-06	NA	mr1789_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
vg1206394265	NA	1.55E-06	mr1982_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