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Detailed information for vg0827835751:

Variant ID: vg0827835751 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 27835751
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, G: 0.04, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TAAGATAAATTTTGAAAACTTTCCAGTACAGATTTGAAAATTTTTAAGTTAAGATTTGAAAAAATATAAAAACTTTCGACTCAGATTTAAAAACTTTCAA[C/G]
TCGAGATTTGAAAACTTTCAACTCCGATTCGAAAACCTTCGACTCATATTCGAAAACTTTCGACTCAGATTCGAAAACTTTCGACTCGAGATTTGAAAAC

Reverse complement sequence

GTTTTCAAATCTCGAGTCGAAAGTTTTCGAATCTGAGTCGAAAGTTTTCGAATATGAGTCGAAGGTTTTCGAATCGGAGTTGAAAGTTTTCAAATCTCGA[G/C]
TTGAAAGTTTTTAAATCTGAGTCGAAAGTTTTTATATTTTTTCAAATCTTAACTTAAAAATTTTCAAATCTGTACTGGAAAGTTTTCAAAATTTATCTTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.10%	23.40%	1.71%	0.74%	NA
All Indica	2759	62.70%	33.60%	2.46%	1.23%	NA
All Japonica	1512	99.50%	0.40%	0.07%	0.00%	NA
Aus	269	39.80%	56.90%	3.35%	0.00%	NA
Indica I	595	67.10%	32.30%	0.67%	0.00%	NA
Indica II	465	80.20%	16.30%	1.94%	1.51%	NA
Indica III	913	49.60%	45.20%	2.96%	2.19%	NA
Indica Intermediate	786	64.20%	31.30%	3.56%	0.89%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.60%	0.20%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	78.90%	16.70%	3.33%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0827835751	C -> G	LOC_Os08g44210.1	downstream_gene_variant ; 1615.0bp to feature; MODIFIER	silent_mutation	Average:17.742; most accessible tissue: Callus, score: 35.689	N	N	N	N
vg0827835751	C -> G	LOC_Os08g44220.1	intron_variant ; MODIFIER	silent_mutation	Average:17.742; most accessible tissue: Callus, score: 35.689	N	N	N	N
vg0827835751	C -> DEL	N	N	silent_mutation	Average:17.742; most accessible tissue: Callus, score: 35.689	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0827835751	1.85E-06	NA	mr1530_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