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Detailed information for vg0112384462:

Variant ID: vg0112384462 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 12384462
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.91, C: 0.09, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

GTCATCACAGAAATAATAGGTGCATGTGAAGAAGCAACCATCTTAGCATGACGACACGGTGTATAAACCAAATCAAGATCTTTCTTAAGTTTAGACAAAC[T/C]
ACGAACAAGATCCAAACCACTTAACCTCGTGAGATGATCAAAACCAACATGTCCAAGTCTACGATGCCAAAACATCACATCTTTACTAAACTTAGCAACC

Reverse complement sequence

GGTTGCTAAGTTTAGTAAAGATGTGATGTTTTGGCATCGTAGACTTGGACATGTTGGTTTTGATCATCTCACGAGGTTAAGTGGTTTGGATCTTGTTCGT[A/G]
GTTTGTCTAAACTTAAGAAAGATCTTGATTTGGTTTATACACCGTGTCGTCATGCTAAGATGGTTGCTTCTTCACATGCACCTATTATTTCTGTGATGAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.80%	3.60%	0.66%	4.87%	NA
All Indica	2759	96.10%	0.10%	0.22%	3.52%	NA
All Japonica	1512	89.20%	10.70%	0.00%	0.07%	NA
Aus	269	43.50%	0.00%	9.29%	47.21%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	96.80%	0.00%	0.43%	2.80%	NA
Indica III	913	95.50%	0.20%	0.33%	3.94%	NA
Indica Intermediate	786	93.50%	0.30%	0.13%	6.11%	NA
Temperate Japonica	767	94.40%	5.60%	0.00%	0.00%	NA
Tropical Japonica	504	93.50%	6.30%	0.00%	0.20%	NA
Japonica Intermediate	241	63.90%	36.10%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	6.70%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0112384462	T -> DEL	LOC_Os01g22050.1	N	frameshift_variant	Average:31.67; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0112384462	T -> C	LOC_Os01g22050.1	missense_variant ; p.Ser591Gly; MODERATE	nonsynonymous_codon ; S591G	Average:31.67; most accessible tissue: Zhenshan97 panicle, score: 52.263	possibly damaging	-1.834	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0112384462	1.71E-06	1.71E-06	mr1312_2	Jap_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
vg0112384462	1.41E-06	1.41E-06	mr1634_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