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Detailed information for vg0711577817:

Variant ID: vg0711577817 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11577817
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: 68. )

Flanking Sequence (100 bp) in Reference Genome:

CATAAGTTAGTTCCCTTTTAACTTAATCTTCAAGTCTAGGTAATTTAAATGGTTTAAGTCTATAGTAAAACAACAGAGTTAGGTCATTTTAAAGCTTCTG[C/T]
TGTAATAGTTAGCCAGAATCTCGTAAATACCCTATTACTTTATGTAATAATATCTCCTTCAAAGCTATGTCTAAATGTATGCAAAGACGATCCAGATTAT

Reverse complement sequence

ATAATCTGGATCGTCTTTGCATACATTTAGACATAGCTTTGAAGGAGATATTATTACATAAAGTAATAGGGTATTTACGAGATTCTGGCTAACTATTACA[G/A]
CAGAAGCTTTAAAATGACCTAACTCTGTTGTTTTACTATAGACTTAAACCATTTAAATTACCTAGACTTGAAGATTAAGTTAAAAGGGAACTAACTTATG

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	37.20%	11.10%	29.07%	22.60%	NA
All Indica	2759	10.20%	17.80%	38.20%	33.74%	NA
All Japonica	1512	82.00%	0.10%	11.64%	6.22%	NA
Aus	269	52.40%	1.90%	34.94%	10.78%	NA
Indica I	595	7.70%	1.80%	46.39%	44.03%	NA
Indica II	465	8.40%	22.80%	40.00%	28.82%	NA
Indica III	913	9.20%	33.00%	30.56%	27.27%	NA
Indica Intermediate	786	14.40%	9.40%	39.82%	36.39%	NA
Temperate Japonica	767	69.90%	0.00%	17.99%	12.13%	NA
Tropical Japonica	504	98.80%	0.20%	0.99%	0.00%	NA
Japonica Intermediate	241	85.50%	0.40%	13.69%	0.41%	NA
VI/Aromatic	96	43.80%	21.90%	34.38%	0.00%	NA
Intermediate	90	61.10%	4.40%	18.89%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0711577817	C -> DEL	N	N	silent_mutation	Average:9.726; most accessible tissue: Callus, score: 33.941	N	N	N	N
vg0711577817	C -> T	LOC_Os07g19530-LOC_Os07g19540	intergenic_region ; MODIFIER	silent_mutation	Average:9.726; most accessible tissue: Callus, score: 33.941	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711577817	NA	8.94E-07	mr1525	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
vg0711577817	NA	4.13E-09	mr1525	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