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Detailed information for vg1121318063:

Variant ID: vg1121318063 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21318063
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

GGGTTTCGTTTATTCTAGGGTGAGCAAAGAAATAATAACAATAACAATAATAAGGTCATAACAAAGGTAAATAGGCATGGCTAATTAAAACAATGATAAC[A/G]
CGGGAATTTAAATAAAGCGATAATGCATTAATTTAAATCAAATTAATTTTATAAACTGGGATTCAATATGCTCAAGGATGATGTGACTTGCCTTGCTCGC

Reverse complement sequence

GCGAGCAAGGCAAGTCACATCATCCTTGAGCATATTGAATCCCAGTTTATAAAATTAATTTGATTTAAATTAATGCATTATCGCTTTATTTAAATTCCCG[T/C]
GTTATCATTGTTTTAATTAGCCATGCCTATTTACCTTTGTTATGACCTTATTATTGTTATTGTTATTATTTCTTTGCTCACCCTAGAATAAACGAAACCC

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	28.20%	26.00%	7.43%	38.43%	NA
All Indica	2759	39.80%	7.90%	6.96%	45.38%	NA
All Japonica	1512	11.70%	64.20%	5.03%	19.05%	NA
Aus	269	12.60%	5.20%	12.64%	69.52%	NA
Indica I	595	10.80%	23.20%	3.87%	62.18%	NA
Indica II	465	38.50%	4.10%	5.38%	52.04%	NA
Indica III	913	56.10%	1.40%	10.62%	31.87%	NA
Indica Intermediate	786	43.60%	6.00%	5.98%	44.40%	NA
Temperate Japonica	767	7.80%	78.60%	2.61%	10.95%	NA
Tropical Japonica	504	16.70%	52.20%	5.75%	25.40%	NA
Japonica Intermediate	241	13.70%	43.60%	11.20%	31.54%	NA
VI/Aromatic	96	4.20%	0.00%	41.67%	54.17%	NA
Intermediate	90	21.10%	27.80%	10.00%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121318063	A -> DEL	N	N	silent_mutation	Average:12.646; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg1121318063	A -> G	LOC_Os11g36220.1	upstream_gene_variant ; 455.0bp to feature; MODIFIER	silent_mutation	Average:12.646; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg1121318063	A -> G	LOC_Os11g36220-LOC_Os11g36230	intergenic_region ; MODIFIER	silent_mutation	Average:12.646; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121318063	NA	2.13E-08	mr1804	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
vg1121318063	8.11E-08	NA	mr1055_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
vg1121318063	3.04E-08	NA	mr1055_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
vg1121318063	2.15E-06	NA	mr1390_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
vg1121318063	2.00E-06	NA	mr1490_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