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Detailed information for vg1111465097:

Variant ID: vg1111465097 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 11465097
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGCAATGGTTTCCAATCAAATAGTGTCTCCAAATCTTTAGCTCATGAACCACGACTGCTAGTTCTAGGTCATGGGTAGGGTAATTTTCCTCGTGTGGTC[G/A]
CAGTTGTCGCGATGCATAAGCCACGTCCTTTCCTTCTTGCATCAGTACTCCTCCCCAGTCCTTGCCTTGATGCATCACAATATATAACAAAGTCTTTCCT

Reverse complement sequence

AGGAAAGACTTTGTTATATATTGTGATGCATCAAGGCAAGGACTGGGGAGGAGTACTGATGCAAGAAGGAAAGGACGTGGCTTATGCATCGCGACAACTG[C/T]
GACCACACGAGGAAAATTACCCTACCCATGACCTAGAACTAGCAGTCGTGGTTCATGAGCTAAAGATTTGGAGACACTATTTGATTGGAAACCATTGCGA

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	43.30%	1.60%	28.80%	26.30%	NA
All Indica	2759	12.00%	2.70%	47.92%	37.37%	NA
All Japonica	1512	95.40%	0.00%	0.53%	4.10%	NA
Aus	269	53.90%	0.00%	5.58%	40.52%	NA
Indica I	595	10.90%	2.00%	61.85%	25.21%	NA
Indica II	465	15.90%	1.10%	23.66%	59.35%	NA
Indica III	913	10.00%	4.40%	50.93%	34.72%	NA
Indica Intermediate	786	13.00%	2.20%	48.22%	36.64%	NA
Temperate Japonica	767	96.60%	0.00%	0.52%	2.87%	NA
Tropical Japonica	504	92.50%	0.00%	0.00%	7.54%	NA
Japonica Intermediate	241	97.50%	0.00%	1.66%	0.83%	NA
VI/Aromatic	96	85.40%	0.00%	3.12%	11.46%	NA
Intermediate	90	51.10%	1.10%	14.44%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1111465097	G -> A	LOC_Os11g19910.1	stop_gained ; p.Arg834*; HIGH	stop_gained	Average:11.162; most accessible tissue: Callus, score: 20.378	N	N	N	N
vg1111465097	G -> DEL	LOC_Os11g19910.1	N	frameshift_variant	Average:11.162; most accessible tissue: Callus, score: 20.378	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1111465097	NA	1.20E-09	mr1005	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
vg1111465097	3.81E-07	4.09E-07	mr1011	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
vg1111465097	2.43E-06	3.15E-06	mr1012	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
vg1111465097	NA	1.33E-21	mr1122	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
vg1111465097	NA	4.80E-07	mr1315	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
vg1111465097	NA	1.69E-06	mr1392	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
vg1111465097	NA	2.59E-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
vg1111465097	NA	2.53E-08	mr1604	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
vg1111465097	NA	2.26E-90	mr1758	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
vg1111465097	NA	3.50E-09	mr1776	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
vg1111465097	NA	3.54E-07	mr1797	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
vg1111465097	NA	3.54E-07	mr1801	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
vg1111465097	NA	2.63E-07	mr1810	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
vg1111465097	NA	2.13E-21	mr1839	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
vg1111465097	NA	4.93E-07	mr1886	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