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Detailed information for vg1216906679:

Variant ID: vg1216906679 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16906679
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.56, A: 0.44, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

TCCACATACTCCCTCCACACCCTCCACACCCTTCGAACTCTCCCCTCCTCTCCTATTTTCTAAAAAATAAGAAACTATAACATCTGCATCAAAAACTAAT[A/C]
TTTGATCCGCTTATGTCTTTACATTCAAAGACACATATCCACTATAATTCAACTTTGAAATAAATGTATCATTTTAGGGCTATATTTTTTTGATTTTTTT

Reverse complement sequence

AAAAAAATCAAAAAAATATAGCCCTAAAATGATACATTTATTTCAAAGTTGAATTATAGTGGATATGTGTCTTTGAATGTAAAGACATAAGCGGATCAAA[T/G]
ATTAGTTTTTGATGCAGATGTTATAGTTTCTTATTTTTTAGAAAATAGGAGAGGAGGGGAGAGTTCGAAGGGTGTGGAGGGTGTGGAGGGAGTATGTGGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	32.30%	7.00%	8.82%	51.90%	NA
All Indica	2759	18.30%	6.90%	12.11%	62.78%	NA
All Japonica	1512	62.50%	1.00%	3.44%	33.07%	NA
Aus	269	9.30%	43.90%	5.95%	40.89%	NA
Indica I	595	32.40%	3.50%	14.12%	49.92%	NA
Indica II	465	11.00%	3.70%	7.10%	78.28%	NA
Indica III	913	13.30%	9.30%	11.83%	65.61%	NA
Indica Intermediate	786	17.70%	8.40%	13.87%	60.05%	NA
Temperate Japonica	767	87.40%	0.10%	1.17%	11.34%	NA
Tropical Japonica	504	34.90%	2.00%	7.34%	55.75%	NA
Japonica Intermediate	241	41.10%	1.70%	2.49%	54.77%	NA
VI/Aromatic	96	13.50%	4.20%	3.12%	79.17%	NA
Intermediate	90	42.20%	5.60%	13.33%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216906679	A -> C	LOC_Os12g28590.1	upstream_gene_variant ; 2337.0bp to feature; MODIFIER	silent_mutation	Average:29.703; most accessible tissue: Callus, score: 62.222	N	N	N	N
vg1216906679	A -> C	LOC_Os12g28580-LOC_Os12g28590	intergenic_region ; MODIFIER	silent_mutation	Average:29.703; most accessible tissue: Callus, score: 62.222	N	N	N	N
vg1216906679	A -> DEL	N	N	silent_mutation	Average:29.703; most accessible tissue: Callus, score: 62.222	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216906679	NA	1.67E-07	mr1227	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
vg1216906679	NA	9.71E-06	mr1269	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
vg1216906679	NA	7.13E-06	mr1511	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