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Detailed information for vg0729047751:

Variant ID: vg0729047751 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 29047751
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

AGCCGGAATATATAATTTGTTTTGATATTAGTATACGTTTAATACTTAAAATGTGCGTCCGTATACTTTAAAAACTTTACACCCAAATAACTAAACACAC[C/T]
CTTGATGTATACTACTTTCGTCCCAAAATATAATAACTTTTGGCTATGAATCTGGATATATAGTTGTCTATACTTATAGCTAAAATTGCTTATATTTTGG

Reverse complement sequence

CCAAAATATAAGCAATTTTAGCTATAAGTATAGACAACTATATATCCAGATTCATAGCCAAAAGTTATTATATTTTGGGACGAAAGTAGTATACATCAAG[G/A]
GTGTGTTTAGTTATTTGGGTGTAAAGTTTTTAAAGTATACGGACGCACATTTTAAGTATTAAACGTATACTAATATCAAAACAAATTATATATTCCGGCT

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	88.30%	1.20%	0.68%	9.84%	NA
All Indica	2759	94.90%	2.00%	0.69%	2.43%	NA
All Japonica	1512	74.20%	0.00%	0.86%	24.93%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	92.10%	6.10%	1.85%	0.00%	NA
Indica II	465	94.00%	0.60%	0.43%	4.95%	NA
Indica III	913	99.30%	0.40%	0.00%	0.22%	NA
Indica Intermediate	786	92.40%	1.50%	0.76%	5.34%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	25.80%	0.00%	2.18%	72.02%	NA
Japonica Intermediate	241	93.40%	0.00%	0.83%	5.81%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	82.20%	0.00%	0.00%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0729047751	C -> DEL	N	N	silent_mutation	Average:57.14; most accessible tissue: Callus, score: 94.157	N	N	N	N
vg0729047751	C -> T	LOC_Os07g48550-LOC_Os07g48560	intergenic_region ; MODIFIER	silent_mutation	Average:57.14; most accessible tissue: Callus, score: 94.157	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0729047751	NA	7.13E-08	mr1201	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
vg0729047751	NA	3.98E-08	mr1219	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
vg0729047751	NA	7.69E-08	mr1274	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
vg0729047751	NA	4.34E-09	mr1585	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
vg0729047751	NA	9.70E-07	mr1765	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
vg0729047751	NA	1.46E-07	mr1201_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
vg0729047751	NA	1.46E-07	mr1219_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
vg0729047751	NA	1.32E-07	mr1274_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