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Detailed information for vg1222749071:

Variant ID: vg1222749071 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22749071
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: 259. )

Flanking Sequence (100 bp) in Reference Genome:

CTTAGTGACCTTTACAATAACTTAGCATTTGGCGCTTGCGTTGCAACGAGATTTTGATTAAAGAAATTATCATTAATCCACTATTGCTATTTTTTTTTCT[G/A]
CATGTATCATCTCTGCTGCATATATTTGTTAATACTTAATAGTATGTGAATCCTTTAGCCTCAAAATATGTTCTTTTTCCTTAAAAAAGAGTTGGTGGCC

Reverse complement sequence

GGCCACCAACTCTTTTTTAAGGAAAAAGAACATATTTTGAGGCTAAAGGATTCACATACTATTAAGTATTAACAAATATATGCAGCAGAGATGATACATG[C/T]
AGAAAAAAAAATAGCAATAGTGGATTAATGATAATTTCTTTAATCAAAATCTCGTTGCAACGCAAGCGCCAAATGCTAAGTTATTGTAAAGGTCACTAAG

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	97.50%	1.20%	0.17%	1.14%	NA
All Indica	2759	97.90%	0.00%	0.18%	1.85%	NA
All Japonica	1512	96.30%	3.60%	0.07%	0.07%	NA
Aus	269	98.50%	0.00%	0.74%	0.74%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	92.90%	0.00%	0.86%	6.24%	NA
Indica III	913	99.70%	0.00%	0.00%	0.33%	NA
Indica Intermediate	786	97.50%	0.00%	0.13%	2.42%	NA
Temperate Japonica	767	93.10%	6.80%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222749071	G -> DEL	N	N	silent_mutation	Average:37.407; most accessible tissue: Callus, score: 53.73	N	N	N	N
vg1222749071	G -> A	LOC_Os12g37130.1	upstream_gene_variant ; 1340.0bp to feature; MODIFIER	silent_mutation	Average:37.407; most accessible tissue: Callus, score: 53.73	N	N	N	N
vg1222749071	G -> A	LOC_Os12g37120-LOC_Os12g37130	intergenic_region ; MODIFIER	silent_mutation	Average:37.407; most accessible tissue: Callus, score: 53.73	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222749071	4.89E-06	NA	mr1060_2	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