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Detailed information for vg0327935681:

Variant ID: vg0327935681 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 27935681
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

ATTATTTTTATGTGCAATTACCAATTTGTTAAAAAGATCTTCGCAGGCGGACGGCACGCTTGCAAAGATAGTAAAAAAGATCTTCGCAGGCGGACCGCCC[G/C]
CCTGCGAAGATCTTTGGCCTATATAAGGGCAAGCCCGCGACGCCAAAATTTCTAAGTCAAGGCGGGAACCCTACAAATTTTGGTGCCGTCAGGCTGCCGA

Reverse complement sequence

TCGGCAGCCTGACGGCACCAAAATTTGTAGGGTTCCCGCCTTGACTTAGAAATTTTGGCGTCGCGGGCTTGCCCTTATATAGGCCAAAGATCTTCGCAGG[C/G]
GGGCGGTCCGCCTGCGAAGATCTTTTTTACTATCTTTGCAAGCGTGCCGTCCGCCTGCGAAGATCTTTTTAACAAATTGGTAATTGCACATAAAAATAAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.30%	7.40%	8.48%	0.74%	NA
All Indica	2759	76.80%	11.20%	11.74%	0.25%	NA
All Japonica	1512	96.00%	0.40%	1.85%	1.72%	NA
Aus	269	87.40%	7.10%	5.58%	0.00%	NA
Indica I	595	71.80%	8.70%	18.99%	0.50%	NA
Indica II	465	80.40%	9.90%	9.46%	0.22%	NA
Indica III	913	79.70%	12.60%	7.56%	0.11%	NA
Indica Intermediate	786	75.10%	12.20%	12.47%	0.25%	NA
Temperate Japonica	767	95.70%	0.10%	1.30%	2.87%	NA
Tropical Japonica	504	96.80%	0.60%	2.58%	0.00%	NA
Japonica Intermediate	241	95.40%	0.80%	2.07%	1.66%	NA
VI/Aromatic	96	62.50%	9.40%	28.12%	0.00%	NA
Intermediate	90	81.10%	8.90%	7.78%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0327935681	G -> C	LOC_Os03g49040.1	upstream_gene_variant ; 1333.0bp to feature; MODIFIER	silent_mutation	Average:40.484; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0327935681	G -> C	LOC_Os03g49030.1	downstream_gene_variant ; 312.0bp to feature; MODIFIER	silent_mutation	Average:40.484; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0327935681	G -> C	LOC_Os03g49030-LOC_Os03g49040	intergenic_region ; MODIFIER	silent_mutation	Average:40.484; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0327935681	G -> DEL	N	N	silent_mutation	Average:40.484; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0327935681	NA	7.41E-08	mr1193	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
vg0327935681	3.19E-07	3.19E-07	mr1459	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
vg0327935681	NA	2.03E-06	mr1731	Ind_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