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Detailed information for vg1114596184:

Variant ID: vg1114596184 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 14596184
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: 295. )

Flanking Sequence (100 bp) in Reference Genome:

GAAATAGCTGAATTCGTAGCACTCTGTGACGTCTGTCAGCGAGTAAAGGCAGAACACCAAAGGCCAGCAGGTTTGCTACAGCCACTTCAGATTCCAGAAT[G/A]
GAAGTGGGAAGAAATCGGAATGGATTTCATCACCGGTTTGCCCAGGACATCATCGGGGCATGATTCTATTTGGGTAGTCGTTGACCGACTCACCAAAGTG

Reverse complement sequence

CACTTTGGTGAGTCGGTCAACGACTACCCAAATAGAATCATGCCCCGATGATGTCCTGGGCAAACCGGTGATGAAATCCATTCCGATTTCTTCCCACTTC[C/T]
ATTCTGGAATCTGAAGTGGCTGTAGCAAACCTGCTGGCCTTTGGTGTTCTGCCTTTACTCGCTGACAGACGTCACAGAGTGCTACGAATTCAGCTATTTC

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	92.90%	2.80%	2.84%	1.42%	NA
All Indica	2759	88.20%	4.90%	4.57%	2.36%	NA
All Japonica	1512	99.70%	0.00%	0.20%	0.13%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	61.50%	15.10%	16.47%	6.89%	NA
Indica II	465	92.00%	5.60%	1.94%	0.43%	NA
Indica III	913	98.20%	0.20%	0.22%	1.31%	NA
Indica Intermediate	786	94.50%	2.00%	2.16%	1.27%	NA
Temperate Japonica	767	99.30%	0.00%	0.39%	0.26%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	0.00%	4.44%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1114596184	G -> A	LOC_Os11g25590.1	stop_gained ; p.Trp970*; HIGH	stop_gained	Average:14.996; most accessible tissue: Minghui63 young leaf, score: 26.082	N	N	N	N
vg1114596184	G -> DEL	LOC_Os11g25590.1	N	frameshift_variant	Average:14.996; most accessible tissue: Minghui63 young leaf, score: 26.082	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1114596184	3.29E-08	5.99E-15	mr1191	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
vg1114596184	6.83E-08	6.78E-12	mr1191	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
vg1114596184	7.14E-09	5.16E-16	mr1644	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
vg1114596184	1.02E-07	1.25E-12	mr1644	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
vg1114596184	1.74E-06	1.37E-20	mr1191_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
vg1114596184	NA	4.52E-15	mr1191_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
vg1114596184	6.26E-06	3.22E-09	mr1662_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
vg1114596184	1.70E-06	6.69E-10	mr1662_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
vg1114596184	NA	2.48E-09	mr1745_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