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Detailed information for vg1117243555:

Variant ID: vg1117243555 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17243555
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: 254. )

Flanking Sequence (100 bp) in Reference Genome:

AGGCCATGATTTTTGCAAGCGGTCATAGGTCCACCTGCAAAACTCGATTTTCGTAGCTATTGCTATTTCTTAACGTCACAGATAGAATCTACAAGCGCAC[G/A]
GAAGATACCGATATAGCACTTTACCCGGGAGTATTCCAAGGTATCGATTTCCACAGGGAACGTGTGTGTCAGCTCTTCTCCAGGTTCATCCAAGGACACG

Reverse complement sequence

CGTGTCCTTGGATGAACCTGGAGAAGAGCTGACACACACGTTCCCTGTGGAAATCGATACCTTGGAATACTCCCGGGTAAAGTGCTATATCGGTATCTTC[C/T]
GTGCGCTTGTAGATTCTATCTGTGACGTTAAGAAATAGCAATAGCTACGAAAATCGAGTTTTGCAGGTGGACCTATGACCGCTTGCAAAAATCATGGCCT

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	98.00%	0.40%	1.08%	0.55%	NA
All Indica	2759	99.10%	0.40%	0.43%	0.00%	NA
All Japonica	1512	96.10%	0.30%	1.98%	1.65%	NA
Aus	269	98.90%	0.00%	1.12%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.70%	0.40%	0.86%	0.00%	NA
Indica III	913	98.80%	0.70%	0.55%	0.00%	NA
Indica Intermediate	786	99.20%	0.40%	0.38%	0.00%	NA
Temperate Japonica	767	98.70%	0.00%	0.39%	0.91%	NA
Tropical Japonica	504	94.00%	0.20%	3.57%	2.18%	NA
Japonica Intermediate	241	92.10%	1.20%	3.73%	2.90%	NA
VI/Aromatic	96	91.70%	1.00%	6.25%	1.04%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg1117243555	G -> A	LOC_Os11g29730.1	downstream_gene_variant ; 1617.0bp to feature; MODIFIER	silent_mutation	Average:58.528; most accessible tissue: Minghui63 flag leaf, score: 74.161	N	N	N	N
vg1117243555	G -> A	LOC_Os11g29720-LOC_Os11g29730	intergenic_region ; MODIFIER	silent_mutation	Average:58.528; most accessible tissue: Minghui63 flag leaf, score: 74.161	N	N	N	N
vg1117243555	G -> DEL	N	N	silent_mutation	Average:58.528; most accessible tissue: Minghui63 flag leaf, score: 74.161	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117243555	5.17E-06	8.83E-07	mr1800_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