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Detailed information for vg0714251796:

Variant ID: vg0714251796 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14251796
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

TCAGATTCATCAACTGTGTCTGTTGGGCCAGGACTTGAGCGAGCGTGGGATTCTCCGCATTGTTGTTATTGTTGTTGTTGTTGGGGCCATTCCCGTTGCT[G/A]
CGAGTGAGCACCATCTGACATAGACAGGAGCACAAGAAGAGAAACAGGGGAAAACTACTTAGGATAGGGAATTAAATTAATTAACTTAACTTTTATTGAT

Reverse complement sequence

ATCAATAAAAGTTAAGTTAATTAATTTAATTCCCTATCCTAAGTAGTTTTCCCCTGTTTCTCTTCTTGTGCTCCTGTCTATGTCAGATGGTGCTCACTCG[C/T]
AGCAACGGGAATGGCCCCAACAACAACAACAATAACAACAATGCGGAGAATCCCACGCTCGCTCAAGTCCTGGCCCAACAGACACAGTTGATGAATCTGA

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	76.90%	0.00%	3.26%	19.83%	NA
All Indica	2759	69.20%	0.00%	2.65%	28.13%	NA
All Japonica	1512	86.00%	0.00%	4.89%	9.06%	NA
Aus	269	95.20%	0.00%	0.37%	4.46%	NA
Indica I	595	79.00%	0.00%	2.18%	18.82%	NA
Indica II	465	68.00%	0.00%	3.23%	28.82%	NA
Indica III	913	58.30%	0.00%	2.08%	39.65%	NA
Indica Intermediate	786	75.30%	0.00%	3.31%	21.37%	NA
Temperate Japonica	767	87.50%	0.00%	1.83%	10.69%	NA
Tropical Japonica	504	86.10%	0.00%	5.56%	8.33%	NA
Japonica Intermediate	241	81.30%	0.00%	13.28%	5.39%	NA
VI/Aromatic	96	92.70%	0.00%	2.08%	5.21%	NA
Intermediate	90	86.70%	1.10%	4.44%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714251796	G -> DEL	LOC_Os07g25010.1	N	frameshift_variant	Average:14.121; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0714251796	G -> A	LOC_Os07g25010.1	synonymous_variant ; p.Arg229Arg; LOW	synonymous_codon	Average:14.121; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714251796	4.52E-07	6.08E-10	mr1053	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
vg0714251796	9.47E-06	8.77E-07	mr1053	Ind_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
vg0714251796	1.46E-06	NA	mr1147	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
vg0714251796	NA	6.26E-06	mr1147	Ind_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
vg0714251796	NA	7.82E-06	mr1283	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
vg0714251796	NA	3.16E-06	mr1500	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
vg0714251796	NA	1.33E-07	mr1709	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
vg0714251796	NA	1.29E-06	mr1709	Ind_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