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Detailed information for vg0726491978:

Variant ID: vg0726491978 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 26491978
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

GCTAGATAGTAAGCAATGTTCTAACATGGCATAGGCATATAATATAAATAATGGGAAAATTGTAACCATGCCATTATAATTTTGCAAAATTTAAGATATG[C/T]
CATCCTGACCCACATGTCATTGACTCATGTGGGTCCTACATGTCATTGAGATACCGATGGCATATCTCAAACTTTGAAAAATTATAATGGTATGGTTACA

Reverse complement sequence

TGTAACCATACCATTATAATTTTTCAAAGTTTGAGATATGCCATCGGTATCTCAATGACATGTAGGACCCACATGAGTCAATGACATGTGGGTCAGGATG[G/A]
CATATCTTAAATTTTGCAAAATTATAATGGCATGGTTACAATTTTCCCATTATTTATATTATATGCCTATGCCATGTTAGAACATTGCTTACTATCTAGC

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	89.80%	9.70%	0.30%	0.23%	NA
All Indica	2759	82.90%	16.30%	0.40%	0.40%	NA
All Japonica	1512	99.70%	0.10%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	96.60%	2.50%	0.84%	0.00%	NA
Indica II	465	92.30%	6.90%	0.22%	0.65%	NA
Indica III	913	67.10%	31.90%	0.33%	0.66%	NA
Indica Intermediate	786	85.40%	14.10%	0.25%	0.25%	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	98.80%	0.40%	0.83%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	92.20%	6.70%	1.11%	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
vg0726491978	C -> DEL	N	N	silent_mutation	Average:28.952; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0726491978	C -> T	LOC_Os07g44340.1	downstream_gene_variant ; 447.0bp to feature; MODIFIER	silent_mutation	Average:28.952; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0726491978	C -> T	LOC_Os07g44330-LOC_Os07g44340	intergenic_region ; MODIFIER	silent_mutation	Average:28.952; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0726491978	NA	2.72E-08	mr1518	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
vg0726491978	NA	9.31E-07	mr1676	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
vg0726491978	NA	5.58E-09	mr1244_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
vg0726491978	NA	2.11E-06	mr1264_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
vg0726491978	NA	7.33E-08	mr1676_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