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Detailed information for vg0706623534:

Variant ID: vg0706623534 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 6623534
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.79, C: 0.21, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

CCATTCATTGCTAGCTTAATTTGGTGGCAATAAATATCTCTGCTGCCAACAATATACACAATATAAAGAGAGTGCCCTCTCCCCGGTCACATTGCCAAAC[C/T]
ATGACTTCACAAGCCCTCATATATCATTGCCTCATTGTTCAGCTCCTTCTGCTCCGAGCTCTTATGTCACAGTGAACTGATGTAGGATTCAAAGGTATCA

Reverse complement sequence

TGATACCTTTGAATCCTACATCAGTTCACTGTGACATAAGAGCTCGGAGCAGAAGGAGCTGAACAATGAGGCAATGATATATGAGGGCTTGTGAAGTCAT[G/A]
GTTTGGCAATGTGACCGGGGAGAGGGCACTCTCTTTATATTGTGTATATTGTTGGCAGCAGAGATATTTATTGCCACCAAATTAAGCTAGCAATGAATGG

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	38.10%	15.20%	2.73%	44.01%	NA
All Indica	2759	8.60%	18.10%	3.73%	69.63%	NA
All Japonica	1512	93.10%	0.20%	0.20%	6.55%	NA
Aus	269	4.50%	73.60%	7.81%	14.13%	NA
Indica I	595	11.30%	19.50%	6.39%	62.86%	NA
Indica II	465	12.70%	4.70%	0.43%	82.15%	NA
Indica III	913	2.50%	21.70%	1.31%	74.48%	NA
Indica Intermediate	786	11.20%	20.60%	6.49%	61.70%	NA
Temperate Japonica	767	87.60%	0.30%	0.26%	11.86%	NA
Tropical Japonica	504	99.40%	0.00%	0.20%	0.40%	NA
Japonica Intermediate	241	97.10%	0.40%	0.00%	2.49%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	58.90%	14.40%	2.22%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0706623534	C -> DEL	N	N	silent_mutation	Average:12.936; most accessible tissue: Callus, score: 78.69	N	N	N	N
vg0706623534	C -> T	LOC_Os07g11920-LOC_Os07g11970	intergenic_region ; MODIFIER	silent_mutation	Average:12.936; most accessible tissue: Callus, score: 78.69	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0706623534	5.55E-06	5.55E-06	mr1656	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
vg0706623534	1.24E-06	1.24E-06	mr1802	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