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Detailed information for vg1121561182:

Variant ID: vg1121561182 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21561182
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.04, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

TTATGATAATTTAAATTTAAATAGTATGTAGAATGGTGATTGAAATGTAAAAAGTAAGGTGGTATGACTTTATGGAAGAAGAAAAGTAGAGAGATAGTTT[G/A]
GACAGTAGATTAATCATTTAAAGGGTAAAAACAATTGATGTGATATGACTTAATTAGAGGAAAAAAGGAGAAAGATAATTTAAACCATAGATTAATCATT

Reverse complement sequence

AATGATTAATCTATGGTTTAAATTATCTTTCTCCTTTTTTCCTCTAATTAAGTCATATCACATCAATTGTTTTTACCCTTTAAATGATTAATCTACTGTC[C/T]
AAACTATCTCTCTACTTTTCTTCTTCCATAAAGTCATACCACCTTACTTTTTACATTTCAATCACCATTCTACATACTATTTAAATTTAAATTATCATAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	32.60%	30.30%	0.28%	36.84%	NA
All Indica	2759	46.10%	6.80%	0.29%	46.86%	NA
All Japonica	1512	4.10%	77.40%	0.26%	18.19%	NA
Aus	269	66.90%	11.20%	0.37%	21.56%	NA
Indica I	595	61.70%	6.60%	0.34%	31.43%	NA
Indica II	465	40.60%	3.70%	0.43%	55.27%	NA
Indica III	913	42.10%	5.80%	0.00%	52.14%	NA
Indica Intermediate	786	42.10%	9.90%	0.51%	47.46%	NA
Temperate Japonica	767	5.70%	85.00%	0.00%	9.26%	NA
Tropical Japonica	504	1.20%	69.80%	0.79%	28.17%	NA
Japonica Intermediate	241	5.00%	69.30%	0.00%	25.73%	NA
VI/Aromatic	96	3.10%	8.30%	0.00%	88.54%	NA
Intermediate	90	25.60%	41.10%	0.00%	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
vg1121561182	G -> A	LOC_Os11g36530.1	upstream_gene_variant ; 4755.0bp to feature; MODIFIER	silent_mutation	Average:17.036; most accessible tissue: Callus, score: 36.581	N	N	N	N
vg1121561182	G -> A	LOC_Os11g36550.1	upstream_gene_variant ; 658.0bp to feature; MODIFIER	silent_mutation	Average:17.036; most accessible tissue: Callus, score: 36.581	N	N	N	N
vg1121561182	G -> A	LOC_Os11g36530-LOC_Os11g36550	intergenic_region ; MODIFIER	silent_mutation	Average:17.036; most accessible tissue: Callus, score: 36.581	N	N	N	N
vg1121561182	G -> DEL	N	N	silent_mutation	Average:17.036; most accessible tissue: Callus, score: 36.581	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121561182	8.81E-07	8.81E-07	mr1438_2	Jap_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
vg1121561182	NA	2.89E-06	mr1559_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
vg1121561182	NA	3.72E-06	mr1561_2	Jap_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
vg1121561182	1.16E-06	1.16E-06	mr1908_2	Jap_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
vg1121561182	1.93E-08	7.34E-10	mr1994_2	Jap_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