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Detailed information for vg1219268495:

Variant ID: vg1219268495 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19268495
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.20, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

CCAACCAAACAAAAAACTGCGATCATCTCATCCACACAACCAATGGAAAGAACGGGACAACCATATTTTCAAAAAAATAGATATATCCAACCTTGATGAT[G/A]
AACCAACAAACCTTAAACTTTCCAACAGACCCAATACTGGCACCGCAGGTTGCCATTGCCGTCTCTCGTTTCGTCCTGGTTCTTCTCATTCCCAACCTCT

Reverse complement sequence

AGAGGTTGGGAATGAGAAGAACCAGGACGAAACGAGAGACGGCAATGGCAACCTGCGGTGCCAGTATTGGGTCTGTTGGAAAGTTTAAGGTTTGTTGGTT[C/T]
ATCATCAAGGTTGGATATATCTATTTTTTTGAAAATATGGTTGTCCCGTTCTTTCCATTGGTTGTGTGGATGAGATGATCGCAGTTTTTTGTTTGGTTGG

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	37.70%	36.90%	0.19%	25.22%	NA
All Indica	2759	5.80%	57.10%	0.25%	36.82%	NA
All Japonica	1512	96.60%	2.40%	0.07%	0.99%	NA
Aus	269	8.20%	39.40%	0.00%	52.42%	NA
Indica I	595	4.00%	54.30%	0.00%	41.68%	NA
Indica II	465	10.30%	27.10%	1.08%	61.51%	NA
Indica III	913	2.50%	72.70%	0.00%	24.75%	NA
Indica Intermediate	786	8.30%	58.90%	0.25%	32.57%	NA
Temperate Japonica	767	98.30%	1.20%	0.13%	0.39%	NA
Tropical Japonica	504	97.60%	1.80%	0.00%	0.60%	NA
Japonica Intermediate	241	88.80%	7.50%	0.00%	3.73%	NA
VI/Aromatic	96	82.30%	10.40%	0.00%	7.29%	NA
Intermediate	90	66.70%	17.80%	1.11%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1219268495	G -> DEL	N	N	silent_mutation	Average:24.681; most accessible tissue: Callus, score: 65.518	N	N	N	N
vg1219268495	G -> A	LOC_Os12g31960.1	downstream_gene_variant ; 4253.0bp to feature; MODIFIER	silent_mutation	Average:24.681; most accessible tissue: Callus, score: 65.518	N	N	N	N
vg1219268495	G -> A	LOC_Os12g31960-LOC_Os12g31980	intergenic_region ; MODIFIER	silent_mutation	Average:24.681; most accessible tissue: Callus, score: 65.518	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219268495	3.21E-06	NA	mr1116	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