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Detailed information for vg1215952216:

Variant ID: vg1215952216 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15952216
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, A: 0.23, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

GGCACATGGTGACATGATGTGGGGTTGTGTCTTGTGGGTACAGTGGTACACCTCTGATCAGAGTAAAACTATTCGAATAGCCGTGCCCGCGGTTATGGGC[A/G]
GGTCTAACAATGTCTTTCGTGATTAGTCTCACACTTCTCATCATAGAAGATGCTATAACTGGTAATAATTTGATTAGCTCCTGGTTTGGAATGGTATATT

Reverse complement sequence

AATATACCATTCCAAACCAGGAGCTAATCAAATTATTACCAGTTATAGCATCTTCTATGATGAGAAGTGTGAGACTAATCACGAAAGACATTGTTAGACC[T/C]
GCCCATAACCGCGGGCACGGCTATTCGAATAGTTTTACTCTGATCAGAGGTGTACCACTGTACCCACAAGACACAACCCCACATCATGTCACCATGTGCC

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	35.70%	25.10%	28.84%	10.41%	NA
All Indica	2759	50.50%	5.30%	34.36%	9.82%	NA
All Japonica	1512	16.50%	62.10%	8.60%	12.83%	NA
Aus	269	5.60%	10.40%	82.53%	1.49%	NA
Indica I	595	37.30%	6.10%	44.37%	12.27%	NA
Indica II	465	48.00%	7.10%	33.98%	10.97%	NA
Indica III	913	64.40%	1.50%	26.18%	7.89%	NA
Indica Intermediate	786	45.90%	8.00%	36.51%	9.54%	NA
Temperate Japonica	767	2.10%	93.90%	1.96%	2.09%	NA
Tropical Japonica	504	40.50%	12.50%	16.87%	30.16%	NA
Japonica Intermediate	241	12.00%	64.70%	12.45%	10.79%	NA
VI/Aromatic	96	9.40%	38.50%	36.46%	15.62%	NA
Intermediate	90	20.00%	40.00%	31.11%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215952216	A -> DEL	N	N	silent_mutation	Average:19.797; most accessible tissue: Minghui63 young leaf, score: 55.178	N	N	N	N
vg1215952216	A -> G	LOC_Os12g27180.1	upstream_gene_variant ; 1171.0bp to feature; MODIFIER	silent_mutation	Average:19.797; most accessible tissue: Minghui63 young leaf, score: 55.178	N	N	N	N
vg1215952216	A -> G	LOC_Os12g27180-LOC_Os12g27190	intergenic_region ; MODIFIER	silent_mutation	Average:19.797; most accessible tissue: Minghui63 young leaf, score: 55.178	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215952216	3.34E-06	NA	mr1295	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
vg1215952216	NA	4.64E-06	mr1718	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