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Detailed information for vg0620560057:

Variant ID: vg0620560057 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20560057
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.85, A: 0.14, T: 0.01, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

TATTATAAAAGTTGTCAAGATTGTCAGAAGTTTGGAGCAATCCAAAGGGCGCCGGCATCGGCTATGAATCCTATTATTAAACCGTGGCCTTTTAAAGGTT[G/A]
GGGAATTGATATGATCGGTATGATTAATCCACCCTCGAGTAAAAGACATAAGTTTATATTGGTGGCAACCGATTATTCTACCAAGTGGGTAGAGGCCATT

Reverse complement sequence

AATGGCCTCTACCCACTTGGTAGAATAATCGGTTGCCACCAATATAAACTTATGTCTTTTACTCGAGGGTGGATTAATCATACCGATCATATCAATTCCC[C/T]
AACCTTTAAAAGGCCACGGTTTAATAATAGGATTCATAGCCGATGCCGGCGCCCTTTGGATTGCTCCAAACTTCTGACAATCTTGACAACTTTTATAATA

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	30.30%	0.40%	3.85%	65.43%	NA
All Indica	2759	6.00%	0.60%	1.56%	91.84%	NA
All Japonica	1512	60.60%	0.00%	7.14%	32.21%	NA
Aus	269	85.50%	0.00%	7.43%	7.06%	NA
Indica I	595	5.50%	0.50%	1.68%	92.27%	NA
Indica II	465	5.20%	0.00%	1.29%	93.55%	NA
Indica III	913	4.40%	0.70%	1.42%	93.54%	NA
Indica Intermediate	786	8.70%	1.00%	1.78%	88.55%	NA
Temperate Japonica	767	80.40%	0.00%	3.26%	16.30%	NA
Tropical Japonica	504	31.00%	0.00%	11.90%	57.14%	NA
Japonica Intermediate	241	59.80%	0.00%	9.54%	30.71%	NA
VI/Aromatic	96	88.50%	1.00%	7.29%	3.12%	NA
Intermediate	90	41.10%	0.00%	4.44%	54.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0620560057	G -> A	LOC_Os06g35260.1	stop_gained ; p.Trp244*; HIGH	stop_gained	Average:15.721; most accessible tissue: Minghui63 flower, score: 20.111	N	N	N	N
vg0620560057	G -> DEL	LOC_Os06g35260.1	N	frameshift_variant	Average:15.721; most accessible tissue: Minghui63 flower, score: 20.111	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620560057	NA	1.15E-21	mr1020	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
vg0620560057	NA	4.72E-15	mr1165	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
vg0620560057	NA	9.62E-07	mr1245	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
vg0620560057	NA	1.07E-12	mr1335	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
vg0620560057	NA	3.71E-09	mr1336	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
vg0620560057	NA	5.24E-08	mr1488	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
vg0620560057	NA	2.13E-08	mr1506	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
vg0620560057	NA	2.60E-06	mr1508	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
vg0620560057	NA	1.03E-06	mr1527	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
vg0620560057	NA	1.10E-07	mr1824	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