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Detailed information for vg1217179451:

Variant ID: vg1217179451 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17179451
Reference Allele: G	Alternative Allele: A,C
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

CTAGTACAAGAAAGAAACTTTACATAACCAATCGTACCAAATTTGGACTCCTTCCAAATTCGACTCCGCATCCCACACGCACACAATACCTCCATCGTAT[G/A,C]
CCATATAGAATCTCCATCAACCACGTGCATCAACTCTAGCCTAAGTATCCCGCATGATCTCTGACCACCACGGACGTCGTCTTATCCCCAAGCCGACTCC

Reverse complement sequence

GGAGTCGGCTTGGGGATAAGACGACGTCCGTGGTGGTCAGAGATCATGCGGGATACTTAGGCTAGAGTTGATGCACGTGGTTGATGGAGATTCTATATGG[C/T,G]
ATACGATGGAGGTATTGTGTGCGTGTGGGATGCGGAGTCGAATTTGGAAGGAGTCCAAATTTGGTACGATTGGTTATGTAAAGTTTCTTTCTTGTACTAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.70%	19.90%	0.49%	2.92%	NA
All Indica	2759	65.00%	32.80%	0.76%	1.45%	NA
All Japonica	1512	93.30%	0.40%	0.07%	6.22%	NA
Aus	269	94.10%	5.20%	0.37%	0.37%	NA
Indica I	595	21.00%	73.90%	2.18%	2.86%	NA
Indica II	465	86.50%	13.10%	0.43%	0.00%	NA
Indica III	913	77.90%	19.90%	0.33%	1.86%	NA
Indica Intermediate	786	70.50%	28.40%	0.38%	0.76%	NA
Temperate Japonica	767	97.30%	0.40%	0.00%	2.35%	NA
Tropical Japonica	504	89.50%	0.20%	0.20%	10.12%	NA
Japonica Intermediate	241	88.80%	0.80%	0.00%	10.37%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	88.90%	7.80%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217179451	G -> C	LOC_Os12g29020.1	downstream_gene_variant ; 3738.0bp to feature; MODIFIER	N	Average:33.805; most accessible tissue: Minghui63 flag leaf, score: 59.244	N	N	N	N
vg1217179451	G -> C	LOC_Os12g29020-LOC_Os12g29030	intergenic_region ; MODIFIER	N	Average:33.805; most accessible tissue: Minghui63 flag leaf, score: 59.244	N	N	N	N
vg1217179451	G -> DEL	N	N	silent_mutation	Average:33.805; most accessible tissue: Minghui63 flag leaf, score: 59.244	N	N	N	N
vg1217179451	G -> A	LOC_Os12g29020.1	downstream_gene_variant ; 3738.0bp to feature; MODIFIER	silent_mutation	Average:33.805; most accessible tissue: Minghui63 flag leaf, score: 59.244	N	N	N	N
vg1217179451	G -> A	LOC_Os12g29020-LOC_Os12g29030	intergenic_region ; MODIFIER	silent_mutation	Average:33.805; most accessible tissue: Minghui63 flag leaf, score: 59.244	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217179451	4.89E-06	1.57E-06	mr1755	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