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Detailed information for vg1220409333:

Variant ID: vg1220409333 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 20409333
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.88, C: 0.12, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

TAATGCTATTTCACTTTCGCTTGTGATATAATCCGAACAGTCACTTAGTTCGGCTATATTTTCAATGATGTCATTGTCTAAACTAGCAACACAATCTGAA[T/C]
CATCACTTGGTTCGGCTATTCCATCATTGTCTAAACTAATAACACAATCCAAACCGTCGCTTGGTTCGGCCATAATGGTTGGTGCATCATTATCCAAGCT

Reverse complement sequence

AGCTTGGATAATGATGCACCAACCATTATGGCCGAACCAAGCGACGGTTTGGATTGTGTTATTAGTTTAGACAATGATGGAATAGCCGAACCAAGTGATG[A/G]
TTCAGATTGTGTTGCTAGTTTAGACAATGACATCATTGAAAATATAGCCGAACTAAGTGACTGTTCGGATTATATCACAAGCGAAAGTGAAATAGCATTA

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	30.60%	15.30%	1.86%	52.26%	NA
All Indica	2759	12.90%	23.80%	0.76%	62.56%	NA
All Japonica	1512	65.70%	1.50%	3.51%	29.37%	NA
Aus	269	13.40%	10.40%	1.12%	75.09%	NA
Indica I	595	34.10%	3.00%	0.67%	62.18%	NA
Indica II	465	11.00%	32.90%	0.65%	55.48%	NA
Indica III	913	0.90%	36.60%	0.77%	61.77%	NA
Indica Intermediate	786	12.00%	19.20%	0.89%	67.94%	NA
Temperate Japonica	767	94.30%	0.30%	0.13%	5.35%	NA
Tropical Japonica	504	21.40%	3.40%	6.15%	69.05%	NA
Japonica Intermediate	241	67.20%	1.20%	8.71%	22.82%	NA
VI/Aromatic	96	19.80%	3.10%	10.42%	66.67%	NA
Intermediate	90	46.70%	14.40%	1.11%	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
vg1220409333	T -> C	LOC_Os12g33840.1	downstream_gene_variant ; 3998.0bp to feature; MODIFIER	silent_mutation	Average:6.643; most accessible tissue: Callus, score: 14.984	N	N	N	N
vg1220409333	T -> C	LOC_Os12g33840-LOC_Os12g33870	intergenic_region ; MODIFIER	silent_mutation	Average:6.643; most accessible tissue: Callus, score: 14.984	N	N	N	N
vg1220409333	T -> DEL	N	N	silent_mutation	Average:6.643; most accessible tissue: Callus, score: 14.984	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220409333	NA	5.14E-06	mr1123	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
vg1220409333	8.48E-06	3.33E-07	mr1815	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
vg1220409333	3.90E-06	NA	mr1847	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
vg1220409333	9.36E-06	9.36E-06	mr1847	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