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Detailed information for vg0415467485:

Variant ID: vg0415467485 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 15467485
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTCTTCCAAGGCATCCCGCGAACCAGTCCTTAATTGCCATGGGCATGACCATCAAAACCATGCACCCACAGCCCACCATTTAATATATTTTAATTAACC[G/A]
ACACCGGAGCGGTGGCATTAACCAACATCATTACTAGAATCTAATATCTATGCATTAATGTAGTCCCCCATTGTGTGCTAGTTGAACTAAGCAAGGCTAA

Reverse complement sequence

TTAGCCTTGCTTAGTTCAACTAGCACACAATGGGGGACTACATTAATGCATAGATATTAGATTCTAGTAATGATGTTGGTTAATGCCACCGCTCCGGTGT[C/T]
GGTTAATTAAAATATATTAAATGGTGGGCTGTGGGTGCATGGTTTTGATGGTCATGCCCATGGCAATTAAGGACTGGTTCGCGGGATGCCTTGGAAGAAC

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	81.30%	0.30%	1.63%	16.74%	NA
All Indica	2759	86.40%	0.40%	1.92%	11.24%	NA
All Japonica	1512	82.30%	0.10%	1.12%	16.47%	NA
Aus	269	17.10%	0.40%	2.23%	80.30%	NA
Indica I	595	94.50%	0.30%	0.50%	4.71%	NA
Indica II	465	80.60%	0.60%	3.01%	15.70%	NA
Indica III	913	84.20%	0.20%	2.63%	12.92%	NA
Indica Intermediate	786	86.30%	0.60%	1.53%	11.58%	NA
Temperate Japonica	767	67.30%	0.30%	2.22%	30.25%	NA
Tropical Japonica	504	99.00%	0.00%	0.00%	0.99%	NA
Japonica Intermediate	241	95.00%	0.00%	0.00%	4.98%	NA
VI/Aromatic	96	91.70%	0.00%	0.00%	8.33%	NA
Intermediate	90	90.00%	0.00%	1.11%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0415467485	G -> DEL	N	N	silent_mutation	Average:52.455; most accessible tissue: Zhenshan97 flag leaf, score: 75.455	N	N	N	N
vg0415467485	G -> A	LOC_Os04g26520.1	upstream_gene_variant ; 719.0bp to feature; MODIFIER	silent_mutation	Average:52.455; most accessible tissue: Zhenshan97 flag leaf, score: 75.455	N	N	N	N
vg0415467485	G -> A	LOC_Os04g26510-LOC_Os04g26520	intergenic_region ; MODIFIER	silent_mutation	Average:52.455; most accessible tissue: Zhenshan97 flag leaf, score: 75.455	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0415467485	2.97E-06	2.98E-06	mr1562	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
vg0415467485	7.02E-06	NA	mr1754	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
vg0415467485	NA	7.36E-06	mr1754	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