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Detailed information for vg1222668845:

Variant ID: vg1222668845 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22668845
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

AGGTGTGGCTCATTTTTTTTTAAGCCACAACTTAGACAAGTGTGGCATAAAAAGTATAGTGAATGGTGGCAAACTTAGTATAGCATCCAAACAGCCTCTA[C/G]
TATTTCATATTAAAATTTAATGGTACTTATATCACATGATGTCTTGGATGTTGTGTAGAAACCATATCTCATGCAAGACATGGTTTCCTTCTCTTTCCTC

Reverse complement sequence

GAGGAAAGAGAAGGAAACCATGTCTTGCATGAGATATGGTTTCTACACAACATCCAAGACATCATGTGATATAAGTACCATTAAATTTTAATATGAAATA[G/C]
TAGAGGCTGTTTGGATGCTATACTAAGTTTGCCACCATTCACTATACTTTTTATGCCACACTTGTCTAAGTTGTGGCTTAAAAAAAAATGAGCCACACCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.80%	2.30%	1.86%	0.00%	NA
All Indica	2759	98.40%	0.60%	1.01%	0.00%	NA
All Japonica	1512	90.10%	6.10%	3.84%	0.00%	NA
Aus	269	99.30%	0.00%	0.74%	0.00%	NA
Indica I	595	93.40%	2.20%	4.37%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.40%	0.25%	0.00%	NA
Temperate Japonica	767	94.80%	0.70%	4.56%	0.00%	NA
Tropical Japonica	504	92.70%	5.40%	1.98%	0.00%	NA
Japonica Intermediate	241	69.70%	24.90%	5.39%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg1222668845	C -> G	LOC_Os12g36970.1	upstream_gene_variant ; 797.0bp to feature; MODIFIER	silent_mutation	Average:51.32; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg1222668845	C -> G	LOC_Os12g36980.1	downstream_gene_variant ; 2151.0bp to feature; MODIFIER	silent_mutation	Average:51.32; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg1222668845	C -> G	LOC_Os12g36970-LOC_Os12g36980	intergenic_region ; MODIFIER	silent_mutation	Average:51.32; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222668845	2.57E-06	2.57E-06	mr1067_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