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Detailed information for vg1220427559:

Variant ID: vg1220427559 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 20427559
Reference Allele: G	Alternative Allele: A
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: 73. )

Flanking Sequence (100 bp) in Reference Genome:

ACAGTCGTAGCCGACTAAGTCTCAAGGTATTTCCTTGATGTACAAGTTGAGAAACAAACCCGAGACACAAATAAAATATTCTATCTATATTTGGTATCCT[G/A]
TATTCAGTCCAAATACCATCGCCGTGTAGATATGGGATATCCATAATCTCCACAGTAGCCCTCACGACCTTTGCAGTCAACCATCATAGCCTTCTCAAAG

Reverse complement sequence

CTTTGAGAAGGCTATGATGGTTGACTGCAAAGGTCGTGAGGGCTACTGTGGAGATTATGGATATCCCATATCTACACGGCGATGGTATTTGGACTGAATA[C/T]
AGGATACCAAATATAGATAGAATATTTTATTTGTGTCTCGGGTTTGTTTCTCAACTTGTACATCAAGGAAATACCTTGAGACTTAGTCGGCTACGACTGT

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	24.30%	7.20%	8.97%	59.52%	NA
All Indica	2759	4.70%	10.20%	11.74%	73.29%	NA
All Japonica	1512	62.90%	0.10%	0.66%	36.31%	NA
Aus	269	11.50%	10.00%	26.02%	52.42%	NA
Indica I	595	6.70%	4.00%	4.54%	84.71%	NA
Indica II	465	5.20%	11.20%	13.33%	70.32%	NA
Indica III	913	2.80%	15.20%	16.32%	65.61%	NA
Indica Intermediate	786	5.20%	8.50%	10.94%	75.32%	NA
Temperate Japonica	767	93.10%	0.00%	0.00%	6.91%	NA
Tropical Japonica	504	15.70%	0.40%	1.39%	82.54%	NA
Japonica Intermediate	241	65.60%	0.00%	1.24%	33.20%	NA
VI/Aromatic	96	7.30%	22.90%	13.54%	56.25%	NA
Intermediate	90	33.30%	6.70%	7.78%	52.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1220427559	G -> DEL	N	N	silent_mutation	Average:17.662; most accessible tissue: Callus, score: 41.191	N	N	N	N
vg1220427559	G -> A	LOC_Os12g33890.1	upstream_gene_variant ; 1073.0bp to feature; MODIFIER	silent_mutation	Average:17.662; most accessible tissue: Callus, score: 41.191	N	N	N	N
vg1220427559	G -> A	LOC_Os12g33859-LOC_Os12g33890	intergenic_region ; MODIFIER	silent_mutation	Average:17.662; most accessible tissue: Callus, score: 41.191	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220427559	NA	4.13E-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
vg1220427559	NA	2.78E-06	mr1371	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
vg1220427559	1.07E-06	8.30E-08	mr1815	Ind_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