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Detailed information for vg1222445637:

Variant ID: vg1222445637 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22445637
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.02, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

GAAATACAGACTATACTCTCCCGTCCCATGAAAAACGAATCTAGGACCGTATGTGACATATTCTAGTACTATGAATCTGAACATATGTATGTCTAGATTC[G/A]
TAGTATTAAAATGTGTCACATCCGGTACTAGGTTATTTTTTTATGGGACGGAGGGAGTATATGTTTCCGTGACGAGCTGAGTGAGCTGTAGCAGGATGCA

Reverse complement sequence

TGCATCCTGCTACAGCTCACTCAGCTCGTCACGGAAACATATACTCCCTCCGTCCCATAAAAAAATAACCTAGTACCGGATGTGACACATTTTAATACTA[C/T]
GAATCTAGACATACATATGTTCAGATTCATAGTACTAGAATATGTCACATACGGTCCTAGATTCGTTTTTCATGGGACGGGAGAGTATAGTCTGTATTTC

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	51.80%	6.70%	3.39%	38.07%	NA
All Indica	2759	32.60%	11.20%	4.24%	51.98%	NA
All Japonica	1512	84.40%	0.10%	1.32%	14.22%	NA
Aus	269	40.50%	0.70%	8.18%	50.56%	NA
Indica I	595	58.50%	2.00%	2.18%	37.31%	NA
Indica II	465	36.80%	14.60%	3.01%	45.59%	NA
Indica III	913	16.80%	14.50%	7.12%	61.66%	NA
Indica Intermediate	786	28.90%	12.30%	3.18%	55.60%	NA
Temperate Japonica	767	87.10%	0.00%	0.65%	12.26%	NA
Tropical Japonica	504	77.60%	0.20%	2.78%	19.44%	NA
Japonica Intermediate	241	90.00%	0.00%	0.41%	9.54%	NA
VI/Aromatic	96	96.90%	0.00%	0.00%	3.12%	NA
Intermediate	90	78.90%	7.80%	1.11%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222445637	G -> DEL	N	N	silent_mutation	Average:24.322; most accessible tissue: Callus, score: 42.977	N	N	N	N
vg1222445637	G -> A	LOC_Os12g36660.1	upstream_gene_variant ; 2140.0bp to feature; MODIFIER	silent_mutation	Average:24.322; most accessible tissue: Callus, score: 42.977	N	N	N	N
vg1222445637	G -> A	LOC_Os12g36640-LOC_Os12g36660	intergenic_region ; MODIFIER	silent_mutation	Average:24.322; most accessible tissue: Callus, score: 42.977	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222445637	2.35E-07	2.35E-07	mr1300	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