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Detailed information for vg0415473298:

Variant ID: vg0415473298 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 15473298
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGCTCACGATGGTCAATCGTGATTGGTTATTAACTAATTGTGAACTAAAACTTGATTAATGGTGGGTTGTGAGCACATGGTTTTGATGGTCGTGCTCAT[A/G]
ACAATTAAGGACCAGTTCACGAGCTACTGTTGTGAGACATTAACCATACTAACGACAAGTCAGAATGGGCAACGGCTAGACACTTTGTATAGCAAGGCTC

Reverse complement sequence

GAGCCTTGCTATACAAAGTGTCTAGCCGTTGCCCATTCTGACTTGTCGTTAGTATGGTTAATGTCTCACAACAGTAGCTCGTGAACTGGTCCTTAATTGT[T/C]
ATGAGCACGACCATCAAAACCATGTGCTCACAACCCACCATTAATCAAGTTTTAGTTCACAATTAGTTAATAACCAATCACGATTGACCATCGTGAGCTA

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	81.70%	0.00%	0.68%	17.56%	NA
All Indica	2759	86.90%	0.00%	0.58%	12.50%	NA
All Japonica	1512	82.00%	0.00%	0.40%	17.59%	NA
Aus	269	21.60%	0.40%	3.72%	74.35%	NA
Indica I	595	94.30%	0.00%	0.00%	5.71%	NA
Indica II	465	81.50%	0.00%	1.08%	17.42%	NA
Indica III	913	85.10%	0.10%	0.55%	14.24%	NA
Indica Intermediate	786	86.50%	0.00%	0.76%	12.72%	NA
Temperate Japonica	767	66.60%	0.00%	0.65%	32.72%	NA
Tropical Japonica	504	99.20%	0.00%	0.00%	0.79%	NA
Japonica Intermediate	241	95.00%	0.00%	0.41%	4.56%	NA
VI/Aromatic	96	91.70%	0.00%	0.00%	8.33%	NA
Intermediate	90	87.80%	0.00%	0.00%	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
vg0415473298	A -> DEL	N	N	silent_mutation	Average:44.604; most accessible tissue: Zhenshan97 young leaf, score: 60.208	N	N	N	N
vg0415473298	A -> G	LOC_Os04g26520.1	downstream_gene_variant ; 4831.0bp to feature; MODIFIER	silent_mutation	Average:44.604; most accessible tissue: Zhenshan97 young leaf, score: 60.208	N	N	N	N
vg0415473298	A -> G	LOC_Os04g26530.1	downstream_gene_variant ; 1574.0bp to feature; MODIFIER	silent_mutation	Average:44.604; most accessible tissue: Zhenshan97 young leaf, score: 60.208	N	N	N	N
vg0415473298	A -> G	LOC_Os04g26520-LOC_Os04g26530	intergenic_region ; MODIFIER	silent_mutation	Average:44.604; most accessible tissue: Zhenshan97 young leaf, score: 60.208	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0415473298	NA	1.74E-06	mr1438	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
vg0415473298	7.14E-07	7.14E-07	mr1313_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
vg0415473298	4.54E-07	4.54E-07	mr1473_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
vg0415473298	2.99E-07	2.99E-07	mr1630_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
vg0415473298	3.95E-07	3.95E-07	mr1848_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