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Detailed information for vg0805018852:

Variant ID: vg0805018852 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 5018852
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: 94. )

Flanking Sequence (100 bp) in Reference Genome:

CAAGGACCTAATTAATTAAAGGAAACGTAATAAGAAATCTAACTGAACGATACTTACAAAATCCAACAACTCATAATAGAGACGTCGAGGGCGTCCAGCT[G/A]
GTATAGTTCATAGATACCCTTGAAATTGATCCAGAGAATATCTTTTCCTTGCAAGAAGTCCGTGTCCCTGATCCTCGCTCCGATCATCTCTCTACCGGTG

Reverse complement sequence

CACCGGTAGAGAGATGATCGGAGCGAGGATCAGGGACACGGACTTCTTGCAAGGAAAAGATATTCTCTGGATCAATTTCAAGGGTATCTATGAACTATAC[C/T]
AGCTGGACGCCCTCGACGTCTCTATTATGAGTTGTTGGATTTTGTAAGTATCGTTCAGTTAGATTTCTTATTACGTTTCCTTTAATTAATTAGGTCCTTG

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	64.80%	7.00%	9.44%	18.71%	NA
All Indica	2759	61.90%	11.10%	13.70%	13.37%	NA
All Japonica	1512	66.60%	1.50%	2.12%	29.83%	NA
Aus	269	78.80%	0.00%	8.55%	12.64%	NA
Indica I	595	92.90%	0.70%	2.02%	4.37%	NA
Indica II	465	40.90%	22.40%	15.27%	21.51%	NA
Indica III	913	47.10%	16.30%	20.70%	15.88%	NA
Indica Intermediate	786	67.90%	6.10%	13.49%	12.47%	NA
Temperate Japonica	767	88.10%	2.60%	1.43%	7.82%	NA
Tropical Japonica	504	32.50%	0.20%	2.98%	64.29%	NA
Japonica Intermediate	241	69.30%	0.40%	2.49%	27.80%	NA
VI/Aromatic	96	80.20%	0.00%	6.25%	13.54%	NA
Intermediate	90	67.80%	5.60%	7.78%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0805018852	G -> A	LOC_Os08g08670.1	stop_gained ; p.Gln410*; HIGH	stop_gained	Average:28.747; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N
vg0805018852	G -> DEL	LOC_Os08g08670.1	N	frameshift_variant	Average:28.747; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0805018852	NA	5.43E-07	mr1944	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
vg0805018852	NA	5.97E-06	mr1362_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
vg0805018852	8.59E-06	3.79E-09	mr1836_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