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Detailed information for vg0727093350:

Variant ID: vg0727093350 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 27093350
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

ATCTATACGCTGTTTATCTCCTAAACTTTTACACTCCTAGATAGTTACTCTCCTAGACCTTTGGTCTTATGTAACTCCCTAGTATTGATTGTAACTCAGC[A/G]
CTAGCATTGATTGTAATTCTGTTATATATATGAGAGTTCACCTCCCCACATTGGTGAGGCATCTATTCCACTTTCTCTACAACAATAAAAGCAGGGCAAG

Reverse complement sequence

CTTGCCCTGCTTTTATTGTTGTAGAGAAAGTGGAATAGATGCCTCACCAATGTGGGGAGGTGAACTCTCATATATATAACAGAATTACAATCAATGCTAG[T/C]
GCTGAGTTACAATCAATACTAGGGAGTTACATAAGACCAAAGGTCTAGGAGAGTAACTATCTAGGAGTGTAAAAGTTTAGGAGATAAACAGCGTATAGAT

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	82.70%	17.00%	0.32%	0.02%	NA
All Indica	2759	75.30%	24.40%	0.25%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	57.60%	39.00%	2.97%	0.37%	NA
Indica I	595	50.30%	49.60%	0.17%	0.00%	NA
Indica II	465	91.00%	8.80%	0.22%	0.00%	NA
Indica III	913	77.20%	22.60%	0.22%	0.00%	NA
Indica Intermediate	786	82.80%	16.80%	0.38%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	98.40%	1.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	0.00%	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
vg0727093350	A -> DEL	N	N	silent_mutation	Average:39.362; most accessible tissue: Minghui63 root, score: 47.894	N	N	N	N
vg0727093350	A -> G	LOC_Os07g45420.1	downstream_gene_variant ; 4104.0bp to feature; MODIFIER	silent_mutation	Average:39.362; most accessible tissue: Minghui63 root, score: 47.894	N	N	N	N
vg0727093350	A -> G	LOC_Os07g45410.1	intron_variant ; MODIFIER	silent_mutation	Average:39.362; most accessible tissue: Minghui63 root, score: 47.894	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0727093350	2.46E-06	2.46E-06	mr1460	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