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Detailed information for vg0516129069:

Variant ID: vg0516129069 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 16129069
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTCTTGAACCGCCATGATAAATTCCTTGTGTGCGAGGTTATACCTCATACGAATAACCTATAAATGTATGAAATTAATTAGTAAACAACAAATCGATAC[G/A]
TACGCAATGAAATTTTGAATTTATTTGTACGTACATTAAGCTCTCTTGTGGTGATGATTTGGTCTGCAAGGCAGTGGCAATACTCGCACACGTAATAGCC

Reverse complement sequence

GGCTATTACGTGTGCGAGTATTGCCACTGCCTTGCAGACCAAATCATCACCACAAGAGAGCTTAATGTACGTACAAATAAATTCAAAATTTCATTGCGTA[C/T]
GTATCGATTTGTTGTTTACTAATTAATTTCATACATTTATAGGTTATTCGTATGAGGTATAACCTCGCACACAAGGAATTTATCATGGCGGTTCAAGAAC

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	55.30%	7.90%	20.63%	16.14%	NA
All Indica	2759	41.20%	13.40%	30.99%	14.32%	NA
All Japonica	1512	76.50%	0.00%	2.78%	20.77%	NA
Aus	269	61.30%	0.00%	23.42%	15.24%	NA
Indica I	595	25.90%	27.60%	32.10%	14.45%	NA
Indica II	465	44.30%	1.90%	32.47%	21.29%	NA
Indica III	913	46.80%	8.80%	31.87%	12.60%	NA
Indica Intermediate	786	44.70%	15.00%	28.24%	12.09%	NA
Temperate Japonica	767	93.20%	0.00%	0.65%	6.13%	NA
Tropical Japonica	504	49.20%	0.00%	6.75%	44.05%	NA
Japonica Intermediate	241	80.10%	0.00%	1.24%	18.67%	NA
VI/Aromatic	96	96.90%	0.00%	3.12%	0.00%	NA
Intermediate	90	70.00%	2.20%	13.33%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0516129069	G -> DEL	N	N	silent_mutation	Average:38.558; most accessible tissue: Callus, score: 61.353	N	N	N	N
vg0516129069	G -> A	LOC_Os05g27680.1	upstream_gene_variant ; 861.0bp to feature; MODIFIER	silent_mutation	Average:38.558; most accessible tissue: Callus, score: 61.353	N	N	N	N
vg0516129069	G -> A	LOC_Os05g27670.1	downstream_gene_variant ; 4284.0bp to feature; MODIFIER	silent_mutation	Average:38.558; most accessible tissue: Callus, score: 61.353	N	N	N	N
vg0516129069	G -> A	LOC_Os05g27690.1	intron_variant ; MODIFIER	silent_mutation	Average:38.558; most accessible tissue: Callus, score: 61.353	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0516129069	NA	9.79E-06	mr1174	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
vg0516129069	2.44E-06	NA	mr1314	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