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Detailed information for vg0521681407:

Variant ID: vg0521681407 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 21681407
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAACTGAGACCCAGTACATCTTTTATTGTAGCGACAAGATACATCTTGGAACAGATCTCGAGTGGATGAAAACGGTGAACCAAAATAATGTCTGGACGGC[A/G]
GATAGACTGACTACATGTGGATGGCCAAAGTGCTCGTTTTGTAGATATACTTATAAAACGGTGTTCCACCTCCTAGTAGACTGCAGATACTCTAGTAGCA

Reverse complement sequence

TGCTACTAGAGTATCTGCAGTCTACTAGGAGGTGGAACACCGTTTTATAAGTATATCTACAAAACGAGCACTTTGGCCATCCACATGTAGTCAGTCTATC[T/C]
GCCGTCCAGACATTATTTTGGTTCACCGTTTTCATCCACTCGAGATCTGTTCCAAGATGTATCTTGTCGCTACAATAAAAGATGTACTGGGTCTCAGTTC

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	96.50%	3.00%	0.47%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	89.70%	8.80%	1.46%	0.00%	NA
Aus	269	100.00%	0.00%	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	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.50%	0.00%	0.00%	NA
Temperate Japonica	767	94.00%	3.90%	2.09%	0.00%	NA
Tropical Japonica	504	87.90%	11.50%	0.60%	0.00%	NA
Japonica Intermediate	241	80.10%	18.70%	1.24%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	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
vg0521681407	A -> G	LOC_Os05g37090-LOC_Os05g37100	intergenic_region ; MODIFIER	silent_mutation	Average:62.659; most accessible tissue: Callus, score: 83.184	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0521681407	6.77E-08	7.67E-07	mr1344_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