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Detailed information for vg0714390906:

Variant ID: vg0714390906 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14390906
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGAGCGAGACAAAGCCGCTCATGACAGGGAAAACTGGAATCGAGGCAAGATTTGCAAGTTGGAGAGTAAGGTGTACCGTCTACAGAAGGAATTAGCTGA[G/A]
CTTAAAGGAGAGACGCCGCCGCCAACACCCAAGCTTCACCTCACCGCAAGGAAGAGAACCTGTCCACCACCTCGTCTCCAGTTAGCTTCGAAGCTTCGCG

Reverse complement sequence

CGCGAAGCTTCGAAGCTAACTGGAGACGAGGTGGTGGACAGGTTCTCTTCCTTGCGGTGAGGTGAAGCTTGGGTGTTGGCGGCGGCGTCTCTCCTTTAAG[C/T]
TCAGCTAATTCCTTCTGTAGACGGTACACCTTACTCTCCAACTTGCAAATCTTGCCTCGATTCCAGTTTTCCCTGTCATGAGCGGCTTTGTCTCGCTCCA

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	73.40%	0.80%	19.26%	6.47%	NA
All Indica	2759	66.40%	1.20%	24.47%	7.87%	NA
All Japonica	1512	93.70%	0.00%	1.39%	4.89%	NA
Aus	269	23.40%	1.50%	71.38%	3.72%	NA
Indica I	595	75.30%	0.30%	18.15%	6.22%	NA
Indica II	465	77.40%	0.40%	11.61%	10.54%	NA
Indica III	913	51.50%	2.50%	36.36%	9.64%	NA
Indica Intermediate	786	70.60%	0.90%	23.03%	5.47%	NA
Temperate Japonica	767	93.60%	0.00%	1.04%	5.35%	NA
Tropical Japonica	504	97.20%	0.00%	1.19%	1.59%	NA
Japonica Intermediate	241	86.70%	0.00%	2.90%	10.37%	NA
VI/Aromatic	96	86.50%	1.00%	12.50%	0.00%	NA
Intermediate	90	83.30%	0.00%	11.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714390906	G -> DEL	LOC_Os07g25190.1	N	frameshift_variant	Average:13.991; most accessible tissue: Callus, score: 32.587	N	N	N	N
vg0714390906	G -> A	LOC_Os07g25190.1	synonymous_variant ; p.Glu122Glu; LOW	synonymous_codon	Average:13.991; most accessible tissue: Callus, score: 32.587	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714390906	4.98E-06	NA	mr1363_2	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
vg0714390906	3.91E-07	1.85E-07	mr1363_2	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