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Detailed information for vg0328919612:

Variant ID: vg0328919612 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 28919612
Reference Allele: T	Alternative Allele: A,C
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.95, C: 0.05, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

TTTGGAAGTTGAAAGTGCTGTTTGCTTTTGACCCCATATATGGCTGTGTTTAGATCCAAACTTCCATCTTTTTTCATTACATCAACCTATCATACACACA[T/A,C]
AACTTTTCAGTCACATCATACCAATTTCAATCCAAACTTTCAACTTTGAAAGGAACTAAATACAGCCTATGTATCATAAGGCTTTTTTGAAGTTTGATCA

Reverse complement sequence

TGATCAAACTTCAAAAAAGCCTTATGATACATAGGCTGTATTTAGTTCCTTTCAAAGTTGAAAGTTTGGATTGAAATTGGTATGATGTGACTGAAAAGTT[A/T,G]
TGTGTGTATGATAGGTTGATGTAATGAAAAAAGATGGAAGTTTGGATCTAAACACAGCCATATATGGGGTCAAAAGCAAACAGCACTTTCAACTTCCAAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.80%	3.00%	1.06%	7.15%	C: 0.06%
All Indica	2759	96.60%	0.30%	0.25%	2.83%	NA
All Japonica	1512	89.40%	8.00%	2.58%	0.00%	NA
Aus	269	7.40%	0.00%	0.37%	91.82%	C: 0.37%
Indica I	595	99.50%	0.20%	0.34%	0.00%	NA
Indica II	465	92.90%	0.60%	0.22%	6.24%	NA
Indica III	913	97.70%	0.00%	0.00%	2.30%	NA
Indica Intermediate	786	95.40%	0.50%	0.51%	3.56%	NA
Temperate Japonica	767	84.20%	11.10%	4.69%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	84.20%	14.50%	1.24%	0.00%	NA
VI/Aromatic	96	83.30%	8.30%	1.04%	7.29%	NA
Intermediate	90	85.60%	3.30%	2.22%	6.67%	C: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0328919612	T -> C	LOC_Os03g50644.1	downstream_gene_variant ; 1906.0bp to feature; MODIFIER	silent_mutation	Average:43.214; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0328919612	T -> C	LOC_Os03g50644-LOC_Os03g50660	intergenic_region ; MODIFIER	silent_mutation	Average:43.214; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0328919612	T -> A	LOC_Os03g50644.1	downstream_gene_variant ; 1906.0bp to feature; MODIFIER	silent_mutation	Average:43.214; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0328919612	T -> A	LOC_Os03g50644-LOC_Os03g50660	intergenic_region ; MODIFIER	silent_mutation	Average:43.214; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0328919612	T -> DEL	N	N	silent_mutation	Average:43.214; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0328919612	NA	7.56E-06	mr1048	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
vg0328919612	NA	2.30E-06	mr1278	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
vg0328919612	NA	8.80E-07	mr1280	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
vg0328919612	NA	9.86E-06	mr1485	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
vg0328919612	1.37E-06	1.37E-06	mr1753	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