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Detailed information for vg1019732665:

Variant ID: vg1019732665 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 19732665
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCCCTCTGTGCTTGTAAAGGAAGTCGTTTAGGACTGTTTTTAAGTCAAATCTTAGGAATATAAATCATGAATAACTCTTAAGTTGTTGAGTTTGAAAAT[G/A]
TAAAAATTATATGAATAGATTTGTCTTGAAAAATATTTTCATAAAAGTATACATATATTACTTTTTAATAGATATTTTTATAGAAACAAGAAATCAAAGT

Reverse complement sequence

ACTTTGATTTCTTGTTTCTATAAAAATATCTATTAAAAAGTAATATATGTATACTTTTATGAAAATATTTTTCAAGACAAATCTATTCATATAATTTTTA[C/T]
ATTTTCAAACTCAACAACTTAAGAGTTATTCATGATTTATATTCCTAAGATTTGACTTAAAAACAGTCCTAAACGACTTCCTTTACAAGCACAGAGGGAG

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	95.50%	3.20%	1.33%	0.00%	NA
All Indica	2759	92.80%	5.10%	2.03%	0.00%	NA
All Japonica	1512	99.50%	0.20%	0.33%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	93.30%	2.40%	4.37%	0.00%	NA
Indica II	465	75.90%	19.40%	4.73%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	94.30%	4.70%	1.02%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	98.60%	0.60%	0.79%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	5.60%	2.22%	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
vg1019732665	G -> A	LOC_Os10g36848.1	intron_variant ; MODIFIER	silent_mutation	Average:44.693; most accessible tissue: Minghui63 root, score: 81.505	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1019732665	5.00E-06	1.26E-06	mr1702	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