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Detailed information for vg1117783091:

Variant ID: vg1117783091 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17783091
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGAAGAAAATATAGGGATTAACTCTAAGAAACAATAAAAAAAAGGACCATCTGCACTGCCGCTACCCTCTCTTTAGTCCCGGTTGTTGTTACCAACCGG[G/A]
ACTAAAGATCTATTTTTAGTCTCGGGTATTTGAACCGAGACTAAAGATATCGATCTTTAGTCCCGGATTCGTACTCCCGGTTGGAAAACCAGGACTATAG

Reverse complement sequence

CTATAGTCCTGGTTTTCCAACCGGGAGTACGAATCCGGGACTAAAGATCGATATCTTTAGTCTCGGTTCAAATACCCGAGACTAAAAATAGATCTTTAGT[C/T]
CCGGTTGGTAACAACAACCGGGACTAAAGAGAGGGTAGCGGCAGTGCAGATGGTCCTTTTTTTTATTGTTTCTTAGAGTTAATCCCTATATTTTCTTCAG

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	91.50%	0.90%	6.24%	1.38%	NA
All Indica	2759	85.70%	1.40%	10.51%	2.36%	NA
All Japonica	1512	99.90%	0.00%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	74.30%	1.70%	18.99%	5.04%	NA
Indica II	465	93.10%	0.60%	5.38%	0.86%	NA
Indica III	913	88.40%	1.90%	8.00%	1.75%	NA
Indica Intermediate	786	86.80%	1.30%	10.05%	1.91%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	1.10%	3.33%	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
vg1117783091	G -> A	LOC_Os11g30560.1	upstream_gene_variant ; 2047.0bp to feature; MODIFIER	silent_mutation	Average:31.962; most accessible tissue: Zhenshan97 flag leaf, score: 39.027	N	N	N	N
vg1117783091	G -> A	LOC_Os11g30552.1	downstream_gene_variant ; 1999.0bp to feature; MODIFIER	silent_mutation	Average:31.962; most accessible tissue: Zhenshan97 flag leaf, score: 39.027	N	N	N	N
vg1117783091	G -> A	LOC_Os11g30552-LOC_Os11g30560	intergenic_region ; MODIFIER	silent_mutation	Average:31.962; most accessible tissue: Zhenshan97 flag leaf, score: 39.027	N	N	N	N
vg1117783091	G -> DEL	N	N	silent_mutation	Average:31.962; most accessible tissue: Zhenshan97 flag leaf, score: 39.027	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117783091	5.89E-06	NA	mr1142	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
vg1117783091	2.28E-06	NA	mr1491	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