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Detailed information for vg0227713751:

Variant ID: vg0227713751 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 27713751
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACCGTTTGTCTTATTCAAAAAATTTAAGTAATTATTAATTATTTTCCTATCATTTGATTCATCGTTAAATATACTTCTATATATACATACAGTTTTACA[T/C]
ATTTTAAAAAAATATTGAATAAGACGAACGGTTAAATATATGCTAAAAAGTCAACGGTGTCAAATATTTAAAAATGGAGGGAGTATTTGTTTAGAGGAAT

Reverse complement sequence

ATTCCTCTAAACAAATACTCCCTCCATTTTTAAATATTTGACACCGTTGACTTTTTAGCATATATTTAACCGTTCGTCTTATTCAATATTTTTTTAAAAT[A/G]
TGTAAAACTGTATGTATATATAGAAGTATATTTAACGATGAATCAAATGATAGGAAAATAATTAATAATTACTTAAATTTTTTGAATAAGACAAACGGTT

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	85.20%	11.80%	2.96%	0.00%	NA
All Indica	2759	99.20%	0.30%	0.47%	0.00%	NA
All Japonica	1512	56.90%	35.10%	8.00%	0.00%	NA
Aus	269	99.30%	0.00%	0.74%	0.00%	NA
Indica I	595	99.00%	0.30%	0.67%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	99.60%	0.30%	0.11%	0.00%	NA
Indica Intermediate	786	98.60%	0.50%	0.89%	0.00%	NA
Temperate Japonica	767	71.60%	17.20%	11.21%	0.00%	NA
Tropical Japonica	504	39.10%	57.10%	3.77%	0.00%	NA
Japonica Intermediate	241	47.30%	46.10%	6.64%	0.00%	NA
VI/Aromatic	96	90.60%	7.30%	2.08%	0.00%	NA
Intermediate	90	85.60%	12.20%	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
vg0227713751	T -> C	LOC_Os02g45540.1	downstream_gene_variant ; 592.0bp to feature; MODIFIER	silent_mutation	Average:82.959; most accessible tissue: Minghui63 panicle, score: 92.078	N	N	N	N
vg0227713751	T -> C	LOC_Os02g45550.1	downstream_gene_variant ; 1063.0bp to feature; MODIFIER	silent_mutation	Average:82.959; most accessible tissue: Minghui63 panicle, score: 92.078	N	N	N	N
vg0227713751	T -> C	LOC_Os02g45540-LOC_Os02g45550	intergenic_region ; MODIFIER	silent_mutation	Average:82.959; most accessible tissue: Minghui63 panicle, score: 92.078	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0227713751	NA	1.69E-06	mr1408	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
vg0227713751	7.86E-06	NA	mr1100_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
vg0227713751	NA	1.55E-06	mr1363_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
vg0227713751	1.81E-06	1.80E-06	mr1645_2	Jap_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
vg0227713751	NA	7.06E-06	mr1665_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
vg0227713751	NA	4.67E-08	mr1683_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
vg0227713751	NA	9.44E-06	mr1687_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