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Detailed information for vg0511470966:

Variant ID: vg0511470966 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 11470966
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACCGCCACCACCATAGCCAGCCAGAGCTGAGCTCTTTGTGTTGCCGTTCCGGCCATCTCCTTCTCCCCCTTTGCTTGACACCACCCTCCCCGGATGCGC[A/G]
TCGCCCGGGAACATCATCCGCCACCAACGTCGCCCATCCCCGGCCACCGGAGCATCGACGCCCTACTCTCTCCCTCTCCTCTGTTACTCGGCTGGAAGGA

Reverse complement sequence

TCCTTCCAGCCGAGTAACAGAGGAGAGGGAGAGAGTAGGGCGTCGATGCTCCGGTGGCCGGGGATGGGCGACGTTGGTGGCGGATGATGTTCCCGGGCGA[T/C]
GCGCATCCGGGGAGGGTGGTGTCAAGCAAAGGGGGAGAAGGAGATGGCCGGAACGGCAACACAAAGAGCTCAGCTCTGGCTGGCTATGGTGGTGGCGGTG

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	87.60%	12.40%	0.00%	0.00%	NA
All Indica	2759	87.10%	12.90%	0.00%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	20.40%	79.60%	0.00%	0.00%	NA
Indica I	595	91.60%	8.40%	0.00%	0.00%	NA
Indica II	465	98.50%	1.50%	0.00%	0.00%	NA
Indica III	913	79.10%	20.90%	0.00%	0.00%	NA
Indica Intermediate	786	86.40%	13.60%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	13.30%	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
vg0511470966	A -> G	LOC_Os05g19660.1	downstream_gene_variant ; 4815.0bp to feature; MODIFIER	silent_mutation	Average:70.472; most accessible tissue: Callus, score: 80.631	N	N	N	N
vg0511470966	A -> G	LOC_Os05g19670.1	downstream_gene_variant ; 2882.0bp to feature; MODIFIER	silent_mutation	Average:70.472; most accessible tissue: Callus, score: 80.631	N	N	N	N
vg0511470966	A -> G	LOC_Os05g19680.1	downstream_gene_variant ; 1450.0bp to feature; MODIFIER	silent_mutation	Average:70.472; most accessible tissue: Callus, score: 80.631	N	N	N	N
vg0511470966	A -> G	LOC_Os05g19670-LOC_Os05g19680	intergenic_region ; MODIFIER	silent_mutation	Average:70.472; most accessible tissue: Callus, score: 80.631	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0511470966	2.63E-06	2.63E-06	mr1412	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
vg0511470966	NA	5.86E-10	mr1499	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