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Detailed information for vg0627078208:

Variant ID: vg0627078208 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 27078208
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTCTTAATTTTGTTTACACTTTTTACAGCTTGGTTGATACATCGCATAATTTTTGTCCAGCTACAACGATAACTGACGAGAAGGAACTGGGGTGAAAAT[G/A]
GGGCAGATATTCCGACCCGAGGCTCGCGGGAGGAATATGAGAGAAAAAATAGGATACCTCATACTATCATAGTTCTAATCTAAATATGGGTTAGGATATG

Reverse complement sequence

CATATCCTAACCCATATTTAGATTAGAACTATGATAGTATGAGGTATCCTATTTTTTCTCTCATATTCCTCCCGCGAGCCTCGGGTCGGAATATCTGCCC[C/T]
ATTTTCACCCCAGTTCCTTCTCGTCAGTTATCGTTGTAGCTGGACAAAAATTATGCGATGTATCAACCAAGCTGTAAAAAGTGTAAACAAAATTAAGAGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.60%	2.70%	0.66%	0.00%	NA
All Indica	2759	99.70%	0.30%	0.00%	0.00%	NA
All Japonica	1512	92.90%	5.10%	2.05%	0.00%	NA
Aus	269	87.00%	13.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.00%	1.00%	0.00%	0.00%	NA
Temperate Japonica	767	96.60%	1.40%	1.96%	0.00%	NA
Tropical Japonica	504	97.00%	2.20%	0.79%	0.00%	NA
Japonica Intermediate	241	72.20%	22.80%	4.98%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0627078208	G -> A	LOC_Os06g44830.1	upstream_gene_variant ; 4549.0bp to feature; MODIFIER	silent_mutation	Average:73.7; most accessible tissue: Callus, score: 85.115	N	N	N	N
vg0627078208	G -> A	LOC_Os06g44810.1	downstream_gene_variant ; 3802.0bp to feature; MODIFIER	silent_mutation	Average:73.7; most accessible tissue: Callus, score: 85.115	N	N	N	N
vg0627078208	G -> A	LOC_Os06g44820.1	downstream_gene_variant ; 1570.0bp to feature; MODIFIER	silent_mutation	Average:73.7; most accessible tissue: Callus, score: 85.115	N	N	N	N
vg0627078208	G -> A	LOC_Os06g44820-LOC_Os06g44830	intergenic_region ; MODIFIER	silent_mutation	Average:73.7; most accessible tissue: Callus, score: 85.115	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0627078208	2.26E-06	7.23E-09	mr1750_2	Jap_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