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Detailed information for vg0801307168:

Variant ID: vg0801307168 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1307168
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

TTAAGTGCAATTTGTTCATCCACAAACGAATGTGTGCTGCCTGAGTCAATAAGCATGATCAGTTCCATTCCCTGCACCCAACCATTCACCTTGATAGACT[G/A]
ATTTGATTCAGTTCCCCACAGAGCTTGTTGAGATATGGTCAATAAAGTGCCATGTTGTTCTGGTGATGTTCCCAATTCAATGTTATCAGAATCACTGTCA

Reverse complement sequence

TGACAGTGATTCTGATAACATTGAATTGGGAACATCACCAGAACAACATGGCACTTTATTGACCATATCTCAACAAGCTCTGTGGGGAACTGAATCAAAT[C/T]
AGTCTATCAAGGTGAATGGTTGGGTGCAGGGAATGGAACTGATCATGCTTATTGACTCAGGCAGCACACATTCGTTTGTGGATGAACAAATTGCACTTAA

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	85.00%	1.30%	1.63%	12.06%	NA
All Indica	2759	78.20%	2.20%	2.65%	16.93%	NA
All Japonica	1512	94.80%	0.00%	0.07%	5.09%	NA
Aus	269	98.10%	0.00%	0.00%	1.86%	NA
Indica I	595	77.80%	4.90%	5.71%	11.60%	NA
Indica II	465	88.80%	2.20%	1.29%	7.74%	NA
Indica III	913	71.40%	0.20%	1.64%	26.73%	NA
Indica Intermediate	786	80.20%	2.50%	2.29%	15.01%	NA
Temperate Japonica	767	90.50%	0.00%	0.13%	9.39%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	91.70%	0.00%	1.04%	7.29%	NA
Intermediate	90	81.10%	1.10%	2.22%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0801307168	G -> A	LOC_Os08g02990.1	stop_gained ; p.Gln217*; HIGH	stop_gained	Average:60.84; most accessible tissue: Zhenshan97 root, score: 77.417	N	N	N	N
vg0801307168	G -> DEL	LOC_Os08g02990.1	N	frameshift_variant	Average:60.84; most accessible tissue: Zhenshan97 root, score: 77.417	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801307168	3.64E-06	7.10E-06	mr1277_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
vg0801307168	NA	1.79E-06	mr1746_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