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Detailed information for vg1206203799:

Variant ID: vg1206203799 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6203799
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, A: 0.10, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

GGTGATCTTCGGCATCGCCTCCACCCTCTCTGGCCGCAGCATCTTCCCCTTCGCCCTAGTCCGCCGCCTCTGCCTCCGCTAGTTGCTCAAGGAGATGCAC[C/A]
TTGGCAGTGGATCGGCCGTCCCTCTGCCAGAACTGTTTACGCTAGGCACGAAGCGCGGGCGAAACGTCCTGCGCACTAACCTCCTAGTCCCCATTCGCAA

Reverse complement sequence

TTGCGAATGGGGACTAGGAGGTTAGTGCGCAGGACGTTTCGCCCGCGCTTCGTGCCTAGCGTAAACAGTTCTGGCAGAGGGACGGCCGATCCACTGCCAA[G/T]
GTGCATCTCCTTGAGCAACTAGCGGAGGCAGAGGCGGCGGACTAGGGCGAAGGGGAAGATGCTGCGGCCAGAGAGGGTGGAGGCGATGCCGAAGATCACC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.60%	14.20%	1.31%	25.96%	NA
All Indica	2759	75.80%	14.80%	0.54%	8.88%	NA
All Japonica	1512	37.40%	3.30%	2.38%	56.88%	NA
Aus	269	21.60%	41.30%	3.35%	33.83%	NA
Indica I	595	72.90%	12.60%	0.67%	13.78%	NA
Indica II	465	83.90%	6.90%	0.65%	8.60%	NA
Indica III	913	78.90%	17.30%	0.22%	3.61%	NA
Indica Intermediate	786	69.60%	18.20%	0.76%	11.45%	NA
Temperate Japonica	767	47.50%	5.50%	1.69%	45.37%	NA
Tropical Japonica	504	18.80%	0.60%	3.57%	76.98%	NA
Japonica Intermediate	241	44.40%	2.10%	2.07%	51.45%	NA
VI/Aromatic	96	12.50%	85.40%	0.00%	2.08%	NA
Intermediate	90	45.60%	20.00%	2.22%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1206203799	C -> DEL	N	N	silent_mutation	Average:13.602; most accessible tissue: Callus, score: 42.107	N	N	N	N
vg1206203799	C -> A	LOC_Os12g11480.1	downstream_gene_variant ; 1494.0bp to feature; MODIFIER	silent_mutation	Average:13.602; most accessible tissue: Callus, score: 42.107	N	N	N	N
vg1206203799	C -> A	LOC_Os12g11490.1	intron_variant ; MODIFIER	silent_mutation	Average:13.602; most accessible tissue: Callus, score: 42.107	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206203799	NA	6.19E-06	mr1336	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
vg1206203799	NA	6.36E-06	mr1346	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
vg1206203799	NA	2.67E-07	mr1585_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
vg1206203799	NA	7.98E-06	mr1864_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