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Detailed information for vg0715251894:

Variant ID: vg0715251894 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15251894
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAATGATGTAGCCTACTTTAGGTTACACTCATCATATTTTACAAAGTAGTCGGTATATCACTCGGATCATGTTATTCAGGTGCCCACCTTATATAGGATG[G/A]
GGGCAGGATTACAAGATAGAAACCTTAACCAATACGGTATCGGTTTCCTAAATCTACTTTACAATATTATCAAACCAGGACTTTAGGCCGTTCCGTAATA

Reverse complement sequence

TATTACGGAACGGCCTAAAGTCCTGGTTTGATAATATTGTAAAGTAGATTTAGGAAACCGATACCGTATTGGTTAAGGTTTCTATCTTGTAATCCTGCCC[C/T]
CATCCTATATAAGGTGGGCACCTGAATAACATGATCCGAGTGATATACCGACTACTTTGTAAAATATGATGAGTGTAACCTAAAGTAGGCTACATCATTG

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	60.00%	1.80%	7.51%	30.70%	NA
All Indica	2759	45.20%	0.40%	9.68%	44.69%	NA
All Japonica	1512	91.40%	4.00%	1.32%	3.31%	NA
Aus	269	21.20%	3.30%	24.16%	51.30%	NA
Indica I	595	31.60%	0.00%	8.07%	60.34%	NA
Indica II	465	28.80%	0.00%	4.52%	66.67%	NA
Indica III	913	56.60%	0.30%	10.41%	32.64%	NA
Indica Intermediate	786	52.00%	1.00%	13.10%	33.84%	NA
Temperate Japonica	767	92.60%	0.00%	1.30%	6.13%	NA
Tropical Japonica	504	94.00%	5.40%	0.60%	0.00%	NA
Japonica Intermediate	241	82.20%	13.70%	2.90%	1.24%	NA
VI/Aromatic	96	89.60%	0.00%	0.00%	10.42%	NA
Intermediate	90	71.10%	3.30%	3.33%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0715251894	G -> DEL	N	N	silent_mutation	Average:17.851; most accessible tissue: Minghui63 root, score: 27.443	N	N	N	N
vg0715251894	G -> A	LOC_Os07g26500-LOC_Os07g26510	intergenic_region ; MODIFIER	silent_mutation	Average:17.851; most accessible tissue: Minghui63 root, score: 27.443	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715251894	1.39E-06	1.39E-06	mr1813	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