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Detailed information for vg1208765892:

Variant ID: vg1208765892 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8765892
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

TGACTAATGCACCTAGTACATTCATGCGCTTAATGAATGAGGTTTTAAGGCCTTTTATTGGACGATTTGTGGTAGTGTACTTTGATGACATATTGATTTA[T/C]
AGCAAGTCTTTCGATGAACACATGGATCATTTACGTGCTGTTTTTAATGCTCTACACGATGCACGTTTGTTTGCTAACCTTGAAAACTGCATCTTTTGCA

Reverse complement sequence

TGCAAAAGATGCAGTTTTCAAGGTTAGCAAACAAACGTGCATCGTGTAGAGCATTAAAAACAGCACGTAAATGATCCATGTGTTCATCGAAAGACTTGCT[A/G]
TAAATCAATATGTCATCAAAGTACACTACCACAAATCGTCCAATAAAAGGCCTTAAAACCTCATTCATTAAGCGCATGAATGTACTAGGTGCATTAGTCA

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	36.00%	7.60%	1.18%	55.25%	NA
All Indica	2759	6.00%	12.30%	1.67%	80.03%	NA
All Japonica	1512	95.20%	0.30%	0.07%	4.43%	NA
Aus	269	6.70%	3.00%	2.97%	87.36%	NA
Indica I	595	6.20%	18.80%	1.51%	73.45%	NA
Indica II	465	9.00%	5.80%	0.86%	84.30%	NA
Indica III	913	2.60%	12.50%	2.08%	82.80%	NA
Indica Intermediate	786	7.90%	11.10%	1.78%	79.26%	NA
Temperate Japonica	767	94.00%	0.30%	0.13%	5.61%	NA
Tropical Japonica	504	96.00%	0.40%	0.00%	3.57%	NA
Japonica Intermediate	241	97.50%	0.00%	0.00%	2.49%	NA
VI/Aromatic	96	27.10%	2.10%	1.04%	69.79%	NA
Intermediate	90	58.90%	3.30%	0.00%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208765892	T -> C	LOC_Os12g15350.1	synonymous_variant ; p.Tyr726Tyr; LOW	synonymous_codon	Average:5.663; most accessible tissue: Callus, score: 14.654	N	N	N	N
vg1208765892	T -> DEL	LOC_Os12g15350.1	N	frameshift_variant	Average:5.663; most accessible tissue: Callus, score: 14.654	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208765892	NA	2.97E-06	mr1477_2	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
vg1208765892	3.78E-06	NA	mr1509_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
vg1208765892	NA	2.90E-06	mr1509_2	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