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Detailed information for vg0614458504:

Variant ID: vg0614458504 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 14458504
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TGGATGATGAAGGCTTTGGTGTCTAGCTCGTGCCTGCCGTCAAGCGCCTGTGGTCGTCGCCCTAGTCTTCCGCTGTTTTTCTTTTGTCTTCATGTGTGCT[G/A]
GGCCTTCACCGCCCATGTAATAAATTAACTATTTATGCTTCCGCTTGTTAAACTCTATATTGTATCAACTTTTGGTGTACCTTGCCTCCTGGGACAAGGA

Reverse complement sequence

TCCTTGTCCCAGGAGGCAAGGTACACCAAAAGTTGATACAATATAGAGTTTAACAAGCGGAAGCATAAATAGTTAATTTATTACATGGGCGGTGAAGGCC[C/T]
AGCACACATGAAGACAAAAGAAAAACAGCGGAAGACTAGGGCGACGACCACAGGCGCTTGACGGCAGGCACGAGCTAGACACCAAAGCCTTCATCATCCA

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	61.80%	16.70%	13.63%	7.91%	NA
All Indica	2759	41.10%	26.70%	21.64%	10.51%	NA
All Japonica	1512	93.10%	0.30%	1.85%	4.76%	NA
Aus	269	84.80%	10.40%	2.97%	1.86%	NA
Indica I	595	34.10%	14.60%	30.59%	20.67%	NA
Indica II	465	22.80%	43.40%	22.58%	11.18%	NA
Indica III	913	53.80%	24.40%	16.54%	5.26%	NA
Indica Intermediate	786	42.50%	28.80%	20.23%	8.52%	NA
Temperate Japonica	767	97.40%	0.10%	0.78%	1.69%	NA
Tropical Japonica	504	86.30%	0.60%	4.17%	8.93%	NA
Japonica Intermediate	241	93.80%	0.00%	0.41%	5.81%	NA
VI/Aromatic	96	96.90%	0.00%	0.00%	3.12%	NA
Intermediate	90	64.40%	18.90%	12.22%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0614458504	G -> A	LOC_Os06g24630.1	upstream_gene_variant ; 1903.0bp to feature; MODIFIER	silent_mutation	Average:18.934; most accessible tissue: Zhenshan97 flag leaf, score: 24.95	N	N	N	N
vg0614458504	G -> A	LOC_Os06g24620.1	intron_variant ; MODIFIER	silent_mutation	Average:18.934; most accessible tissue: Zhenshan97 flag leaf, score: 24.95	N	N	N	N
vg0614458504	G -> DEL	N	N	silent_mutation	Average:18.934; most accessible tissue: Zhenshan97 flag leaf, score: 24.95	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0614458504	NA	1.57E-06	mr1042_2	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
vg0614458504	6.04E-06	8.39E-06	mr1559_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
vg0614458504	NA	5.35E-06	mr1950_2	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