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Detailed information for vg0804827547:

Variant ID: vg0804827547 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 4827547
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTTCTGATGAGGAGCAGCAATATGTCAACGTGCAGGTGGAGCACGTGATGATCAGGAAACTGAAATTGTTGGTAATGATGTTCATGATACTGTTCAGCA[C/T]
TCACCTCCTGTTTTGCAGCCACAAGATGAACCTATTGCACATCGCAGAACAAAGAGGAGTTGTGGAGCTCCAGTCCGCCTTATTGAGGAATGTGATATGG

Reverse complement sequence

CCATATCACATTCCTCAATAAGGCGGACTGGAGCTCCACAACTCCTCTTTGTTCTGCGATGTGCAATAGGTTCATCTTGTGGCTGCAAAACAGGAGGTGA[G/A]
TGCTGAACAGTATCATGAACATCATTACCAACAATTTCAGTTTCCTGATCATCACGTGCTCCACCTGCACGTTGACATATTGCTGCTCCTCATCAGAACC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.60%	3.70%	10.98%	13.75%	NA
All Indica	2759	57.10%	6.20%	17.58%	19.10%	NA
All Japonica	1512	96.60%	0.10%	0.40%	2.98%	NA
Aus	269	75.10%	0.00%	7.43%	17.47%	NA
Indica I	595	36.10%	0.50%	25.88%	37.48%	NA
Indica II	465	73.30%	9.70%	10.11%	6.88%	NA
Indica III	913	62.40%	8.50%	15.66%	13.36%	NA
Indica Intermediate	786	57.10%	5.90%	17.94%	19.08%	NA
Temperate Japonica	767	99.60%	0.00%	0.13%	0.26%	NA
Tropical Japonica	504	90.70%	0.00%	0.99%	8.33%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	81.20%	0.00%	5.21%	13.54%	NA
Intermediate	90	75.60%	1.10%	3.33%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0804827547	C -> T	LOC_Os08g08380.1	downstream_gene_variant ; 4604.0bp to feature; MODIFIER	silent_mutation	Average:9.734; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N
vg0804827547	C -> T	LOC_Os08g08370.1	intron_variant ; MODIFIER	silent_mutation	Average:9.734; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N
vg0804827547	C -> DEL	N	N	silent_mutation	Average:9.734; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0804827547	9.80E-07	NA	mr1528	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
vg0804827547	7.68E-07	4.33E-07	mr1528	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