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Detailed information for vg1208959876:

Variant ID: vg1208959876 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8959876
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, G: 0.20, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

TTACGGGCACGTAACACAAACACGAGAGACAACGTCTCTGTATCTACGTCTGTTATGTGGGTTATCACTTACACGGATAAAAAGCCTCTATGATGTGGAT[C/G]
ATCACACACGTTGATTCCAGCCGCGCGTCCATGAGTTGATTTTTCGGGCTAAAAAAACCCAAAAAAATATATCATATTTTAATGTAAATCCATACACGGT

Reverse complement sequence

ACCGTGTATGGATTTACATTAAAATATGATATATTTTTTTGGGTTTTTTTAGCCCGAAAAATCAACTCATGGACGCGCGGCTGGAATCAACGTGTGTGAT[G/C]
ATCCACATCATAGAGGCTTTTTATCCGTGTAAGTGATAACCCACATAACAGACGTAGATACAGAGACGTTGTCTCTCGTGTTTGTGTTACGTGCCCGTAA

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	72.80%	26.80%	0.42%	0.00%	NA
All Indica	2759	56.20%	43.10%	0.69%	0.00%	NA
All Japonica	1512	98.40%	1.50%	0.07%	0.00%	NA
Aus	269	88.10%	11.90%	0.00%	0.00%	NA
Indica I	595	38.00%	60.30%	1.68%	0.00%	NA
Indica II	465	54.40%	44.70%	0.86%	0.00%	NA
Indica III	913	67.50%	32.40%	0.11%	0.00%	NA
Indica Intermediate	786	57.90%	41.60%	0.51%	0.00%	NA
Temperate Japonica	767	98.00%	1.80%	0.13%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	82.20%	17.80%	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
vg1208959876	C -> G	LOC_Os12g15670.1	upstream_gene_variant ; 2103.0bp to feature; MODIFIER	silent_mutation	Average:47.17; most accessible tissue: Minghui63 root, score: 74.812	N	N	N	N
vg1208959876	C -> G	LOC_Os12g15680.1	upstream_gene_variant ; 901.0bp to feature; MODIFIER	silent_mutation	Average:47.17; most accessible tissue: Minghui63 root, score: 74.812	N	N	N	N
vg1208959876	C -> G	LOC_Os12g15670-LOC_Os12g15680	intergenic_region ; MODIFIER	silent_mutation	Average:47.17; most accessible tissue: Minghui63 root, score: 74.812	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208959876	NA	9.90E-06	mr1037	Ind_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
vg1208959876	NA	9.89E-06	mr1100	Ind_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
vg1208959876	NA	1.51E-08	mr1425	Ind_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
vg1208959876	2.66E-07	NA	mr1055_2	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
vg1208959876	NA	1.95E-06	mr1864_2	Ind_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