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Detailed information for vg1219406217:

Variant ID: vg1219406217 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19406217
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TGCCACCACCACCCCCTGAATCATATAATCGCTGGCGGTTGCATGCAAGGTATGTGTTAACACCCAAATTTGGCAATAAAGATGGAAAATAGGGAAACAC[G/A]
GCCAGATTTGGAAGAGATCCGAACTTGCCATGTAGGGCCGGTTTGACCAGTAACATGTAGCCGGTCAAACCGACAGAGTCCGATTCCGAGTCTAATTTGT

Reverse complement sequence

ACAAATTAGACTCGGAATCGGACTCTGTCGGTTTGACCGGCTACATGTTACTGGTCAAACCGGCCCTACATGGCAAGTTCGGATCTCTTCCAAATCTGGC[C/T]
GTGTTTCCCTATTTTCCATCTTTATTGCCAAATTTGGGTGTTAACACATACCTTGCATGCAACCGCCAGCGATTATATGATTCAGGGGGTGGTGGTGGCA

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	69.10%	30.70%	0.15%	0.13%	NA
All Indica	2759	48.40%	51.30%	0.22%	0.18%	NA
All Japonica	1512	98.70%	1.20%	0.07%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	59.80%	40.20%	0.00%	0.00%	NA
Indica II	465	63.90%	35.70%	0.22%	0.22%	NA
Indica III	913	30.90%	68.70%	0.11%	0.33%	NA
Indica Intermediate	786	50.80%	48.60%	0.51%	0.13%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	95.00%	4.60%	0.41%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	86.70%	12.20%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1219406217	G -> DEL	N	N	silent_mutation	Average:37.227; most accessible tissue: Callus, score: 59.617	N	N	N	N
vg1219406217	G -> A	LOC_Os12g32160.1	intron_variant ; MODIFIER	silent_mutation	Average:37.227; most accessible tissue: Callus, score: 59.617	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219406217	3.55E-06	NA	mr1458	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