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Detailed information for vg0612044015:

Variant ID: vg0612044015 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 12044015
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

CTGGCCGCACCCTCTGCGCCGCTGCCTGTCGTCGAGCGCTGCCGCCCGCCATGCCCCTCCGCGCCAGCCGCCGCGCGGCCCTCCGTGCTACCGCCAGCCG[C/T]
GCCTCCCCACATCCACCGCTCGCTCCACTGCTGCTCGAGAGGATAGGATAGAGAGAGGAATGGGAGAGATAGAGAGAGGAAAGGGAGATGATAAGAAAAG

Reverse complement sequence

CTTTTCTTATCATCTCCCTTTCCTCTCTCTATCTCTCCCATTCCTCTCTCTATCCTATCCTCTCGAGCAGCAGTGGAGCGAGCGGTGGATGTGGGGAGGC[G/A]
CGGCTGGCGGTAGCACGGAGGGCCGCGCGGCGGCTGGCGCGGAGGGGCATGGCGGGCGGCAGCGCTCGACGACAGGCAGCGGCGCAGAGGGTGCGGCCAG

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	87.20%	12.60%	0.21%	0.00%	NA
All Indica	2759	82.40%	17.30%	0.29%	0.00%	NA
All Japonica	1512	98.30%	1.70%	0.00%	0.00%	NA
Aus	269	95.20%	4.80%	0.00%	0.00%	NA
Indica I	595	99.50%	0.30%	0.17%	0.00%	NA
Indica II	465	95.90%	3.70%	0.43%	0.00%	NA
Indica III	913	60.80%	38.90%	0.33%	0.00%	NA
Indica Intermediate	786	86.60%	13.10%	0.25%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	96.00%	4.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	33.30%	66.70%	0.00%	0.00%	NA
Intermediate	90	81.10%	16.70%	2.22%	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
vg0612044015	C -> T	LOC_Os06g20850-LOC_Os06g20860	intergenic_region ; MODIFIER	silent_mutation	Average:62.86; most accessible tissue: Zhenshan97 young leaf, score: 76.099	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0612044015	NA	2.03E-08	mr1068	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
vg0612044015	2.95E-06	NA	mr1078	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
vg0612044015	1.30E-07	3.11E-10	mr1078	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
vg0612044015	NA	6.70E-07	mr1094	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
vg0612044015	NA	1.69E-06	mr1111	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
vg0612044015	NA	3.56E-06	mr1121	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
vg0612044015	NA	1.37E-07	mr1144	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
vg0612044015	NA	9.09E-08	mr1068_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
vg0612044015	1.86E-06	4.44E-10	mr1078_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
vg0612044015	NA	2.53E-06	mr1121_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
vg0612044015	NA	4.41E-07	mr1144_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
vg0612044015	NA	3.23E-06	mr1211_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