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Detailed information for vg0415538057:

Variant ID: vg0415538057 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 15538057
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATGAAATGTTTTTGTGGAGTGATTTTTATTGGGTTTGACATCACAGAGGTGAATAGATGTATTTTCTAAGATTAACACATTTGGTTTCATAATAATTAG[C/A]
GTAATTATGATTTCTTTATGAATTTTACAAGTTATAACGTGTTGTAGGCATATAGTGTTCTACATGTATATGTCTTTGGAGTTTTATGTCCAGAACATGT

Reverse complement sequence

ACATGTTCTGGACATAAAACTCCAAAGACATATACATGTAGAACACTATATGCCTACAACACGTTATAACTTGTAAAATTCATAAAGAAATCATAATTAC[G/T]
CTAATTATTATGAAACCAAATGTGTTAATCTTAGAAAATACATCTATTCACCTCTGTGATGTCAAACCCAATAAAAATCACTCCACAAAAACATTTCATA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.40%	11.00%	1.86%	19.66%	NA
All Indica	2759	72.50%	12.40%	1.74%	13.34%	NA
All Japonica	1512	67.20%	10.80%	2.31%	19.71%	NA
Aus	269	8.60%	0.40%	1.12%	89.96%	NA
Indica I	595	90.10%	0.50%	2.02%	7.39%	NA
Indica II	465	69.70%	5.80%	2.15%	22.37%	NA
Indica III	913	58.80%	26.50%	1.86%	12.81%	NA
Indica Intermediate	786	76.80%	8.90%	1.15%	13.10%	NA
Temperate Japonica	767	48.00%	11.60%	3.65%	36.77%	NA
Tropical Japonica	504	89.70%	9.10%	0.20%	0.99%	NA
Japonica Intermediate	241	81.30%	11.60%	2.49%	4.56%	NA
VI/Aromatic	96	84.40%	6.20%	0.00%	9.38%	NA
Intermediate	90	73.30%	11.10%	2.22%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0415538057	C -> DEL	N	N	silent_mutation	Average:37.464; most accessible tissue: Zhenshan97 young leaf, score: 53.314	N	N	N	N
vg0415538057	C -> A	LOC_Os04g26630.1	downstream_gene_variant ; 1112.0bp to feature; MODIFIER	silent_mutation	Average:37.464; most accessible tissue: Zhenshan97 young leaf, score: 53.314	N	N	N	N
vg0415538057	C -> A	LOC_Os04g26640.1	downstream_gene_variant ; 2970.0bp to feature; MODIFIER	silent_mutation	Average:37.464; most accessible tissue: Zhenshan97 young leaf, score: 53.314	N	N	N	N
vg0415538057	C -> A	LOC_Os04g26630-LOC_Os04g26640	intergenic_region ; MODIFIER	silent_mutation	Average:37.464; most accessible tissue: Zhenshan97 young leaf, score: 53.314	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0415538057	NA	9.83E-06	mr1391_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
vg0415538057	NA	5.73E-06	mr1566_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
vg0415538057	4.56E-08	4.54E-08	mr1919_2	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