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Detailed information for vg1222586644:

Variant ID: vg1222586644 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22586644
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

GTGTTTGGTGGAGCATTTAACTATTTGTCACTTTTACATTTGGCATTTAACTATTTGCCACCGCTATCTCAATAACACGTGGGTCCACATGTGTATATGA[C/T]
ATGTGGGTTCAGTGTCAAATAGTTAAATATCTCGTGTTTGATGGCTATAGATCAGTGTAAATGTCACTAAGAAATATTTGTGCAGTCCCTTATTTTGCTA

Reverse complement sequence

TAGCAAAATAAGGGACTGCACAAATATTTCTTAGTGACATTTACACTGATCTATAGCCATCAAACACGAGATATTTAACTATTTGACACTGAACCCACAT[G/A]
TCATATACACATGTGGACCCACGTGTTATTGAGATAGCGGTGGCAAATAGTTAAATGCCAAATGTAAAAGTGACAAATAGTTAAATGCTCCACCAAACAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.00%	9.40%	0.61%	0.00%	NA
All Indica	2759	92.40%	7.40%	0.25%	0.00%	NA
All Japonica	1512	91.50%	7.30%	1.12%	0.00%	NA
Aus	269	59.10%	39.40%	1.49%	0.00%	NA
Indica I	595	96.60%	2.70%	0.67%	0.00%	NA
Indica II	465	95.70%	4.10%	0.22%	0.00%	NA
Indica III	913	90.10%	9.90%	0.00%	0.00%	NA
Indica Intermediate	786	89.70%	10.10%	0.25%	0.00%	NA
Temperate Japonica	767	99.10%	0.10%	0.78%	0.00%	NA
Tropical Japonica	504	80.20%	18.10%	1.79%	0.00%	NA
Japonica Intermediate	241	91.30%	7.90%	0.83%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	77.80%	21.10%	1.11%	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
vg1222586644	C -> T	LOC_Os12g36830.1	downstream_gene_variant ; 4672.0bp to feature; MODIFIER	silent_mutation	Average:43.38; most accessible tissue: Zhenshan97 young leaf, score: 66.32	N	N	N	N
vg1222586644	C -> T	LOC_Os12g36840.1	downstream_gene_variant ; 82.0bp to feature; MODIFIER	silent_mutation	Average:43.38; most accessible tissue: Zhenshan97 young leaf, score: 66.32	N	N	N	N
vg1222586644	C -> T	LOC_Os12g36840-LOC_Os12g36850	intergenic_region ; MODIFIER	silent_mutation	Average:43.38; most accessible tissue: Zhenshan97 young leaf, score: 66.32	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222586644	9.24E-06	9.24E-06	mr1589	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1222586644	2.14E-06	2.14E-06	mr1918	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
vg1222586644	NA	1.10E-06	mr1124_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251