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Detailed information for vg0627586702:

Variant ID: vg0627586702 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 27586702
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCAAAACCTCATACTACTTGGGGCTCAATCTTTTAGGGTATTCTGCTTTAATAATAGAGTTCTTGCTAATTATGTCATACCCCTATAGTTGACATCATG[A/T]
CATGGAATGTTCATGGGTTAAATAGACCGGGTAGAAGAGCAACGGTTAGAGAAACGCTGCAAACGGCGAAGCCCCACATCGCCTACCTGCAAGAGACAAA

Reverse complement sequence

TTTGTCTCTTGCAGGTAGGCGATGTGGGGCTTCGCCGTTTGCAGCGTTTCTCTAACCGTTGCTCTTCTACCCGGTCTATTTAACCCATGAACATTCCATG[T/A]
CATGATGTCAACTATAGGGGTATGACATAATTAGCAAGAACTCTATTATTAAAGCAGAATACCCTAAAAGATTGAGCCCCAAGTAGTATGAGGTTTTGAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.70%	15.80%	5.46%	0.00%	NA
All Indica	2759	92.00%	3.10%	4.86%	0.00%	NA
All Japonica	1512	49.50%	43.00%	7.54%	0.00%	NA
Aus	269	96.30%	1.10%	2.60%	0.00%	NA
Indica I	595	80.00%	7.90%	12.10%	0.00%	NA
Indica II	465	91.60%	3.40%	4.95%	0.00%	NA
Indica III	913	99.30%	0.30%	0.33%	0.00%	NA
Indica Intermediate	786	92.90%	2.50%	4.58%	0.00%	NA
Temperate Japonica	767	16.80%	74.10%	9.13%	0.00%	NA
Tropical Japonica	504	87.50%	8.70%	3.77%	0.00%	NA
Japonica Intermediate	241	73.90%	15.80%	10.37%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	8.90%	3.33%	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
vg0627586702	A -> T	LOC_Os06g45560.1	intron_variant ; MODIFIER	silent_mutation	Average:51.894; most accessible tissue: Callus, score: 69.322	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0627586702	1.57E-06	NA	mr1554	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
vg0627586702	4.33E-06	5.73E-07	mr1554	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
vg0627586702	NA	1.04E-06	mr1554_2	Jap_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
vg0627586702	NA	4.15E-06	mr1977_2	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