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Detailed information for vg0716448920:

Variant ID: vg0716448920 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 16448920
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.69, A: 0.31, others allele: 0.00, population size: 65. )

Flanking Sequence (100 bp) in Reference Genome:

TATATGCTTGACATGTAGGTGCCACCATGACAATGGCACGTCAACGCATGGAGCGGTTTTGAACCCGTTAGGACCTATATGACACACATAACAAGTTTAG[A/G]
GACATAAAAATGCATTTTCGGAGTTCAGGGATCTAGATGACACATATACTTCACTCAAAATTAGATGGCACCAGTCTATGGCACCCATTGCCAGCTGAAA

Reverse complement sequence

TTTCAGCTGGCAATGGGTGCCATAGACTGGTGCCATCTAATTTTGAGTGAAGTATATGTGTCATCTAGATCCCTGAACTCCGAAAATGCATTTTTATGTC[T/C]
CTAAACTTGTTATGTGTGTCATATAGGTCCTAACGGGTTCAAAACCGCTCCATGCGTTGACGTGCCATTGTCATGGTGGCACCTACATGTCAAGCATATA

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	51.40%	46.00%	1.23%	1.38%	NA
All Indica	2759	28.90%	67.70%	2.07%	1.34%	NA
All Japonica	1512	97.80%	0.40%	0.00%	1.79%	NA
Aus	269	5.60%	94.40%	0.00%	0.00%	NA
Indica I	595	12.80%	81.20%	5.71%	0.34%	NA
Indica II	465	76.60%	23.40%	0.00%	0.00%	NA
Indica III	913	12.00%	85.90%	1.31%	0.77%	NA
Indica Intermediate	786	32.60%	62.50%	1.40%	3.56%	NA
Temperate Japonica	767	96.20%	0.30%	0.00%	3.52%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	64.40%	33.30%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0716448920	A -> DEL	N	N	silent_mutation	Average:48.082; most accessible tissue: Minghui63 young leaf, score: 66.656	N	N	N	N
vg0716448920	A -> G	LOC_Os07g28170.1	intron_variant ; MODIFIER	silent_mutation	Average:48.082; most accessible tissue: Minghui63 young leaf, score: 66.656	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0716448920	NA	9.49E-13	mr1069	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
vg0716448920	NA	4.85E-13	mr1149	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
vg0716448920	NA	1.26E-18	mr1441	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
vg0716448920	NA	5.64E-07	mr1441	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
vg0716448920	NA	5.11E-14	mr1874	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
vg0716448920	NA	3.58E-06	mr1074_2	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
vg0716448920	NA	3.42E-28	mr1441_2	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
vg0716448920	NA	1.51E-11	mr1918_2	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