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Detailed information for vg1221791160:

Variant ID: vg1221791160 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21791160
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

GGTGCAGAATTCAAGTTGCTATGCTGCAGCAGCTGCAGGAAGACGTTCAGTCCAGCAGTGTGCAGCAGCTTGGTCTCTGTCGTCGTTTGCATTTCGGCGT[G/C]
CGGCCGTCCTTCTGTTTGGGGAATTGGCGATAGAAACGATCGACCGTCCTCCTTAATTGGCCTTGCCAACGATTACTTAATTACCCTCTCACCTAAATTA

Reverse complement sequence

TAATTTAGGTGAGAGGGTAATTAAGTAATCGTTGGCAAGGCCAATTAAGGAGGACGGTCGATCGTTTCTATCGCCAATTCCCCAAACAGAAGGACGGCCG[C/G]
ACGCCGAAATGCAAACGACGACAGAGACCAAGCTGCTGCACACTGCTGGACTGAACGTCTTCCTGCAGCTGCTGCAGCATAGCAACTTGAATTCTGCACC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.40%	20.80%	0.78%	0.00%	NA
All Indica	2759	73.40%	26.20%	0.36%	0.00%	NA
All Japonica	1512	82.10%	16.10%	1.79%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	49.70%	49.20%	1.01%	0.00%	NA
Indica II	465	86.70%	13.10%	0.22%	0.00%	NA
Indica III	913	80.20%	19.60%	0.22%	0.00%	NA
Indica Intermediate	786	75.70%	24.20%	0.13%	0.00%	NA
Temperate Japonica	767	95.30%	2.60%	2.09%	0.00%	NA
Tropical Japonica	504	71.60%	28.00%	0.40%	0.00%	NA
Japonica Intermediate	241	62.20%	34.00%	3.73%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg1221791160	G -> C	LOC_Os12g35770-LOC_Os12g35790	intergenic_region ; MODIFIER	silent_mutation	Average:64.177; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221791160	5.17E-06	NA	mr1079	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
vg1221791160	1.49E-06	NA	mr1491	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
vg1221791160	3.55E-06	2.25E-07	mr1932	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