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Detailed information for vg0222271516:

Variant ID: vg0222271516 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22271516
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCTATAATATACCGACGACTTTATCAATTGTTCTACAATACGCTATTGGGTTGGGCCTTTTTTTTCAAAAATACCTAAAATATCCTTAGAGACATACAA[G/A]
ATTAACAATTGATTTATCTCATTAGAAGTTTCAAAAAAATATGAAAAGTTTTATGTGGCCTTGTTACACAACATGGAAGTTTGTATAATGTTTCAAGTTT

Reverse complement sequence

AAACTTGAAACATTATACAAACTTCCATGTTGTGTAACAAGGCCACATAAAACTTTTCATATTTTTTTGAAACTTCTAATGAGATAAATCAATTGTTAAT[C/T]
TTGTATGTCTCTAAGGATATTTTAGGTATTTTTGAAAAAAAAGGCCCAACCCAATAGCGTATTGTAGAACAATTGATAAAGTCGTCGGTATATTATAGAA

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	86.90%	2.80%	3.47%	6.88%	NA
All Indica	2759	80.90%	2.10%	5.51%	11.49%	NA
All Japonica	1512	99.30%	0.10%	0.26%	0.33%	NA
Aus	269	78.80%	20.10%	1.12%	0.00%	NA
Indica I	595	78.80%	0.70%	9.41%	11.09%	NA
Indica II	465	63.70%	1.30%	7.53%	27.53%	NA
Indica III	913	95.00%	0.70%	1.86%	2.52%	NA
Indica Intermediate	786	76.50%	5.20%	5.60%	12.72%	NA
Temperate Japonica	767	99.50%	0.00%	0.26%	0.26%	NA
Tropical Japonica	504	99.40%	0.00%	0.20%	0.40%	NA
Japonica Intermediate	241	98.80%	0.40%	0.41%	0.41%	NA
VI/Aromatic	96	81.20%	18.80%	0.00%	0.00%	NA
Intermediate	90	91.10%	0.00%	5.56%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0222271516	G -> A	LOC_Os02g36890.1	downstream_gene_variant ; 1274.0bp to feature; MODIFIER	silent_mutation	Average:27.286; most accessible tissue: Callus, score: 66.752	N	N	N	N
vg0222271516	G -> A	LOC_Os02g36890-LOC_Os02g36910	intergenic_region ; MODIFIER	silent_mutation	Average:27.286; most accessible tissue: Callus, score: 66.752	N	N	N	N
vg0222271516	G -> DEL	N	N	silent_mutation	Average:27.286; most accessible tissue: Callus, score: 66.752	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222271516	1.82E-07	NA	mr1098_2	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
vg0222271516	1.03E-06	NA	mr1098_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
vg0222271516	3.67E-07	NA	mr1099_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
vg0222271516	2.23E-07	NA	mr1099_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
vg0222271516	1.21E-07	NA	mr1113_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
vg0222271516	2.81E-07	1.25E-16	mr1114_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
vg0222271516	8.80E-08	NA	mr1117_2	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
vg0222271516	1.68E-08	1.88E-17	mr1119_2	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
vg0222271516	4.11E-07	NA	mr1120_2	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
vg0222271516	1.99E-06	NA	mr1120_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
vg0222271516	3.90E-09	NA	mr1123_2	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
vg0222271516	7.05E-08	1.00E-06	mr1123_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
vg0222271516	2.91E-08	NA	mr1150_2	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
vg0222271516	8.79E-07	NA	mr1150_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
vg0222271516	5.60E-09	NA	mr1240_2	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
vg0222271516	6.98E-08	NA	mr1242_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
vg0222271516	7.59E-06	1.22E-06	mr1242_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
vg0222271516	3.50E-09	NA	mr1247_2	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
vg0222271516	6.78E-08	8.08E-06	mr1247_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
vg0222271516	NA	2.10E-06	mr1378_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
vg0222271516	3.71E-08	NA	mr1496_2	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
vg0222271516	1.34E-06	NA	mr1936_2	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
vg0222271516	NA	2.53E-06	mr1968_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