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Detailed information for vg0913012156:

Variant ID: vg0913012156 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 13012156
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.75, C: 0.26, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

CAACTGTTGTGGTCTATTTCATTGTAGATGGTACCTATTTAAAATCAGATTTTCTAATTCTAGTGACCTTACCCATGTTTATAAATTGCTCAATGCCCAT[G/C]
CATATCTTGCTCATTGTTAGTCATTTTGGAAGTTTCAGATATTGGTGGATGGCCCCTTATTGATAAGTTGTTACATGATATCATGTTGGAAGTTCAATCT

Reverse complement sequence

AGATTGAACTTCCAACATGATATCATGTAACAACTTATCAATAAGGGGCCATCCACCAATATCTGAAACTTCCAAAATGACTAACAATGAGCAAGATATG[C/G]
ATGGGCATTGAGCAATTTATAAACATGGGTAAGGTCACTAGAATTAGAAAATCTGATTTTAAATAGGTACCATCTACAATGAAATAGACCACAACAGTTG

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	94.60%	5.40%	0.06%	0.00%	NA
All Indica	2759	93.90%	6.00%	0.11%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	90.30%	9.70%	0.00%	0.00%	NA
Indica III	913	93.10%	6.60%	0.33%	0.00%	NA
Indica Intermediate	786	92.20%	7.80%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	30.20%	69.80%	0.00%	0.00%	NA
Intermediate	90	85.60%	14.40%	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
vg0913012156	G -> C	LOC_Os09g21510.1	intron_variant ; MODIFIER	silent_mutation	Average:46.093; most accessible tissue: Callus, score: 70.029	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0913012156	NA	1.37E-07	mr1354	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
vg0913012156	2.06E-06	8.36E-09	mr1377	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
vg0913012156	NA	1.03E-10	mr1570	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
vg0913012156	NA	1.04E-06	mr1958	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