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Detailed information for vg0715416146:

Variant ID: vg0715416146 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15416146
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.88, T: 0.12, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GGAAACGCCAATACTCCCTCAATCCCAATATATGTTTATTCTAGTATAGATGTGATAGCTTATCATTGATGTAACTTATATAAGTAGTTATCTAGATTGA[T/C]
AGAGGTAGTGATTAAGTGTTTTACGTAAAACGAGGTGGTAATAATGTGTGATTAATTGAGTTTTAATTATTACATACTTGAAAAATGGATTAATTTGATA

Reverse complement sequence

TATCAAATTAATCCATTTTTCAAGTATGTAATAATTAAAACTCAATTAATCACACATTATTACCACCTCGTTTTACGTAAAACACTTAATCACTACCTCT[A/G]
TCAATCTAGATAACTACTTATATAAGTTACATCAATGATAAGCTATCACATCTATACTAGAATAAACATATATTGGGATTGAGGGAGTATTGGCGTTTCC

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	75.20%	22.80%	1.95%	0.00%	NA
All Indica	2759	88.40%	9.40%	2.25%	0.00%	NA
All Japonica	1512	47.90%	50.90%	1.26%	0.00%	NA
Aus	269	88.50%	8.20%	3.35%	0.00%	NA
Indica I	595	86.10%	9.20%	4.71%	0.00%	NA
Indica II	465	87.50%	11.40%	1.08%	0.00%	NA
Indica III	913	94.10%	5.40%	0.55%	0.00%	NA
Indica Intermediate	786	84.10%	12.80%	3.05%	0.00%	NA
Temperate Japonica	767	13.70%	85.50%	0.78%	0.00%	NA
Tropical Japonica	504	89.90%	8.70%	1.39%	0.00%	NA
Japonica Intermediate	241	68.90%	28.60%	2.49%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	70.00%	27.80%	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
vg0715416146	T -> C	LOC_Os07g26690-LOC_Os07g26700	intergenic_region ; MODIFIER	silent_mutation	Average:54.803; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715416146	NA	3.23E-07	mr1657	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
vg0715416146	NA	9.25E-08	mr1977	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
vg0715416146	NA	1.90E-07	mr1265_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
vg0715416146	3.67E-06	3.01E-08	mr1528_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
vg0715416146	NA	9.87E-07	mr1582_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