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Detailed information for vg0721076186:

Variant ID: vg0721076186 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 21076186
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.86, G: 0.14, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

CTTGCACGTTAATATATTAGAAGAAAAACAACGTACATCGGTAACACGCCTAAACGATTACAGGGGTAGGCGGTACAGTATGACCATGTCTGCAATCTCC[G/A]
ATTCATGGCACACCTCGAAGATTGACCGGAGATTTGTGATGTTGACTAACACTCGAAGTTTGATGAGCAGAAGAAAATCGCGAACTTGTAATAAATGTTA

Reverse complement sequence

TAACATTTATTACAAGTTCGCGATTTTCTTCTGCTCATCAAACTTCGAGTGTTAGTCAACATCACAAATCTCCGGTCAATCTTCGAGGTGTGCCATGAAT[C/T]
GGAGATTGCAGACATGGTCATACTGTACCGCCTACCCCTGTAATCGTTTAGGCGTGTTACCGATGTACGTTGTTTTTCTTCTAATATATTAACGTGCAAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	27.40%	23.10%	0.53%	48.96%	NA
All Indica	2759	12.30%	8.70%	0.87%	78.11%	NA
All Japonica	1512	47.70%	50.90%	0.00%	1.39%	NA
Aus	269	73.20%	0.70%	0.37%	25.65%	NA
Indica I	595	10.60%	3.20%	0.84%	85.38%	NA
Indica II	465	6.20%	15.50%	0.86%	77.42%	NA
Indica III	913	15.60%	10.10%	0.66%	73.71%	NA
Indica Intermediate	786	13.50%	7.30%	1.15%	78.12%	NA
Temperate Japonica	767	48.50%	50.60%	0.00%	0.91%	NA
Tropical Japonica	504	58.70%	40.70%	0.00%	0.60%	NA
Japonica Intermediate	241	22.00%	73.40%	0.00%	4.56%	NA
VI/Aromatic	96	13.50%	50.00%	0.00%	36.46%	NA
Intermediate	90	28.90%	33.30%	0.00%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0721076186	G -> DEL	N	N	silent_mutation	Average:13.262; most accessible tissue: Callus, score: 88.124	N	N	N	N
vg0721076186	G -> A	LOC_Os07g35190.1	downstream_gene_variant ; 2466.0bp to feature; MODIFIER	silent_mutation	Average:13.262; most accessible tissue: Callus, score: 88.124	N	N	N	N
vg0721076186	G -> A	LOC_Os07g35200.1	downstream_gene_variant ; 717.0bp to feature; MODIFIER	silent_mutation	Average:13.262; most accessible tissue: Callus, score: 88.124	N	N	N	N
vg0721076186	G -> A	LOC_Os07g35210.1	downstream_gene_variant ; 2918.0bp to feature; MODIFIER	silent_mutation	Average:13.262; most accessible tissue: Callus, score: 88.124	N	N	N	N
vg0721076186	G -> A	LOC_Os07g35200-LOC_Os07g35210	intergenic_region ; MODIFIER	silent_mutation	Average:13.262; most accessible tissue: Callus, score: 88.124	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0721076186	1.65E-06	9.57E-07	mr1397_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