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Detailed information for vg0227382414:

Variant ID: vg0227382414 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 27382414
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.03, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

GCAGTATCCCTGCATAGATGGTTCACCCCTGAGTGAGGCAGGTGCGCTACCGTGGGACAACCGTTGAGGTAGGGCCGAGAGGCGTGCCCTACATCGGTGT[C/T]
GCCATTGGTAGGACTGCCATGAGTGTGTGAGAGAGATAACTTAACTTGAATCTTAATTTAATATGTGTATGAGACTTCCCTTTCCCGGGAGCGCCAGAAC

Reverse complement sequence

GTTCTGGCGCTCCCGGGAAAGGGAAGTCTCATACACATATTAAATTAAGATTCAAGTTAAGTTATCTCTCTCACACACTCATGGCAGTCCTACCAATGGC[G/A]
ACACCGATGTAGGGCACGCCTCTCGGCCCTACCTCAACGGTTGTCCCACGGTAGCGCACCTGCCTCACTCAGGGGTGAACCATCTATGCAGGGATACTGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.00%	39.70%	3.32%	0.00%	NA
All Indica	2759	88.10%	6.90%	4.97%	0.00%	NA
All Japonica	1512	0.70%	99.30%	0.00%	0.00%	NA
Aus	269	81.80%	11.50%	6.69%	0.00%	NA
Indica I	595	90.80%	4.20%	5.04%	0.00%	NA
Indica II	465	88.60%	5.80%	5.59%	0.00%	NA
Indica III	913	89.30%	7.00%	3.72%	0.00%	NA
Indica Intermediate	786	84.60%	9.40%	5.98%	0.00%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	1.40%	98.60%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	33.30%	64.40%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0227382414	C -> T	LOC_Os02g45140.1	upstream_gene_variant ; 2749.0bp to feature; MODIFIER	silent_mutation	Average:20.524; most accessible tissue: Minghui63 root, score: 40.262	N	N	N	N
vg0227382414	C -> T	LOC_Os02g45150.1	upstream_gene_variant ; 4512.0bp to feature; MODIFIER	silent_mutation	Average:20.524; most accessible tissue: Minghui63 root, score: 40.262	N	N	N	N
vg0227382414	C -> T	LOC_Os02g45150.2	upstream_gene_variant ; 4502.0bp to feature; MODIFIER	silent_mutation	Average:20.524; most accessible tissue: Minghui63 root, score: 40.262	N	N	N	N
vg0227382414	C -> T	LOC_Os02g45140-LOC_Os02g45150	intergenic_region ; MODIFIER	silent_mutation	Average:20.524; most accessible tissue: Minghui63 root, score: 40.262	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0227382414	3.86E-06	NA	mr1699_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