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Detailed information for vg0514727249:

Variant ID: vg0514727249 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 14727249
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.07, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

GCGCGGCTCGCTGGATGGGATGGCTGTAGGAGTAGGAAACGGAGGGGAGGGCGAAACTATTGAATGGGTTGGATTGGAAGGAGGGACTGTGAAGATGGTC[G/A]
GCGACTAGCAGTGAAGAGGCTCGGTGGAGTGTGGTCATTATTTGGTTGCCGGCAGCGACCAAATCGACGGTGGAGGAGGCTCGGGATGGGTTTGGTAGGG

Reverse complement sequence

CCCTACCAAACCCATCCCGAGCCTCCTCCACCGTCGATTTGGTCGCTGCCGGCAACCAAATAATGACCACACTCCACCGAGCCTCTTCACTGCTAGTCGC[C/T]
GACCATCTTCACAGTCCCTCCTTCCAATCCAACCCATTCAATAGTTTCGCCCTCCCCTCCGTTTCCTACTCCTACAGCCATCCCATCCAGCGAGCCGCGC

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	52.10%	47.30%	0.08%	0.57%	NA
All Indica	2759	79.90%	19.30%	0.07%	0.72%	NA
All Japonica	1512	7.90%	92.00%	0.07%	0.07%	NA
Aus	269	39.00%	61.00%	0.00%	0.00%	NA
Indica I	595	80.00%	19.30%	0.17%	0.50%	NA
Indica II	465	70.50%	28.20%	0.00%	1.29%	NA
Indica III	913	84.30%	15.60%	0.00%	0.11%	NA
Indica Intermediate	786	80.20%	18.40%	0.13%	1.27%	NA
Temperate Japonica	767	2.90%	97.10%	0.00%	0.00%	NA
Tropical Japonica	504	17.70%	82.10%	0.00%	0.20%	NA
Japonica Intermediate	241	3.30%	96.30%	0.41%	0.00%	NA
VI/Aromatic	96	0.00%	100.00%	0.00%	0.00%	NA
Intermediate	90	36.70%	55.60%	1.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0514727249	G -> DEL	N	N	silent_mutation	Average:79.234; most accessible tissue: Zhenshan97 young leaf, score: 90.175	N	N	N	N
vg0514727249	G -> A	LOC_Os05g25360.1	downstream_gene_variant ; 3773.0bp to feature; MODIFIER	silent_mutation	Average:79.234; most accessible tissue: Zhenshan97 young leaf, score: 90.175	N	N	N	N
vg0514727249	G -> A	LOC_Os05g25370.1	intron_variant ; MODIFIER	silent_mutation	Average:79.234; most accessible tissue: Zhenshan97 young leaf, score: 90.175	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0514727249	2.57E-06	9.45E-08	mr1790	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
vg0514727249	NA	3.67E-06	mr1320_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