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Detailed information for vg0508262368:

Variant ID: vg0508262368 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 8262368
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

GGTGGTGTCACTTAGGTCTGTGAACTTAAAATTTGCACATTTCGTTCCGTGAACTTGGTTTAATATATCATCTCGATCCAAACGTCCTTTGACCGTCAAT[G/A]
TGGCAATGCCACGTAGGCAATATTTTTGCTCTCAGCCCCCTCCACATCGCAACACGTCACATATATCTCCTTGTAGCTATATAGTGACAGTGTGACACCA

Reverse complement sequence

TGGTGTCACACTGTCACTATATAGCTACAAGGAGATATATGTGACGTGTTGCGATGTGGAGGGGGCTGAGAGCAAAAATATTGCCTACGTGGCATTGCCA[C/T]
ATTGACGGTCAAAGGACGTTTGGATCGAGATGATATATTAAACCAAGTTCACGGAACGAAATGTGCAAATTTTAAGTTCACAGACCTAAGTGACACCACC

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	45.80%	34.00%	2.07%	18.15%	NA
All Indica	2759	20.30%	57.00%	2.97%	19.72%	NA
All Japonica	1512	92.50%	0.40%	0.86%	6.22%	NA
Aus	269	21.20%	2.60%	0.00%	76.21%	NA
Indica I	595	28.70%	58.50%	1.68%	11.09%	NA
Indica II	465	28.00%	43.70%	0.65%	27.74%	NA
Indica III	913	8.20%	60.10%	4.82%	26.83%	NA
Indica Intermediate	786	23.50%	60.10%	3.18%	13.23%	NA
Temperate Japonica	767	91.70%	0.30%	0.78%	7.30%	NA
Tropical Japonica	504	97.60%	0.60%	0.99%	0.79%	NA
Japonica Intermediate	241	84.60%	0.40%	0.83%	14.11%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	60.00%	24.40%	3.33%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0508262368	G -> DEL	N	N	silent_mutation	Average:53.947; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N
vg0508262368	G -> A	LOC_Os05g14540-LOC_Os05g14560	intergenic_region ; MODIFIER	silent_mutation	Average:53.947; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0508262368	NA	5.10E-11	mr1195	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
vg0508262368	NA	3.97E-08	mr1593	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
vg0508262368	2.89E-07	NA	mr1593_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
vg0508262368	3.40E-08	3.19E-13	mr1593_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