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Detailed information for vg0427745854:

Variant ID: vg0427745854 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 27745854
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

TCCATCTTGGACCAGGCCATATGCAATATTTTCACTTTAGGCAAGGGTTTGTTACCATCTTTGCACATTGGGCCACTATTCTATCAATCTGTCAGTCTAT[C/T]
CGTTTCCATTTGCTAGCTGACTGCCACCACTACTGCACTACGCAAGCGGCAAGCCGTTGCTTCTTCGGGCATTCACCAACTCCGGCAATGCATCCGAGAG

Reverse complement sequence

CTCTCGGATGCATTGCCGGAGTTGGTGAATGCCCGAAGAAGCAACGGCTTGCCGCTTGCGTAGTGCAGTAGTGGTGGCAGTCAGCTAGCAAATGGAAACG[G/A]
ATAGACTGACAGATTGATAGAATAGTGGCCCAATGTGCAAAGATGGTAACAAACCCTTGCCTAAAGTGAAAATATTGCATATGGCCTGGTCCAAGATGGA

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	53.60%	46.00%	0.25%	0.08%	NA
All Indica	2759	83.40%	16.10%	0.36%	0.14%	NA
All Japonica	1512	0.50%	99.50%	0.00%	0.00%	NA
Aus	269	74.00%	26.00%	0.00%	0.00%	NA
Indica I	595	80.30%	19.20%	0.34%	0.17%	NA
Indica II	465	91.40%	8.20%	0.22%	0.22%	NA
Indica III	913	83.40%	16.40%	0.22%	0.00%	NA
Indica Intermediate	786	81.00%	18.10%	0.64%	0.25%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	0.40%	99.60%	0.00%	0.00%	NA
Japonica Intermediate	241	0.80%	99.20%	0.00%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	30.00%	67.80%	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
vg0427745854	C -> DEL	N	N	silent_mutation	Average:47.731; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0427745854	C -> T	LOC_Os04g46820.1	downstream_gene_variant ; 2120.0bp to feature; MODIFIER	silent_mutation	Average:47.731; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0427745854	C -> T	LOC_Os04g46820-LOC_Os04g46830	intergenic_region ; MODIFIER	silent_mutation	Average:47.731; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0427745854	NA	1.90E-06	mr1873	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
vg0427745854	NA	3.31E-06	mr1329_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
vg0427745854	NA	3.96E-06	mr1543_2	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
vg0427745854	NA	4.24E-15	mr1579_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
vg0427745854	NA	5.69E-08	mr1690_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
vg0427745854	2.67E-06	9.46E-08	mr1745_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