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Detailed information for vg0115147411:

Variant ID: vg0115147411 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 15147411
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.70, T: 0.30, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

GATGGCATTTTGACGCTTATTTAATTTGGTTCATTTTTTTTTCTGCTCCTGTGTTGCAACCTGCATGTTATTGGTGTCCTCCTGTGTATTTCCTGAATGA[G/T]
TTCTTGGAGATGGATATGTATGCCTTATTTATGATAATTGTTTGCAGTGAAGCATGTTAATTAGATTGATTCTGTACTTTCAGTGCGAGGCACATTTGTT

Reverse complement sequence

AACAAATGTGCCTCGCACTGAAAGTACAGAATCAATCTAATTAACATGCTTCACTGCAAACAATTATCATAAATAAGGCATACATATCCATCTCCAAGAA[C/A]
TCATTCAGGAAATACACAGGAGGACACCAATAACATGCAGGTTGCAACACAGGAGCAGAAAAAAAAATGAACCAAATTAAATAAGCGTCAAAATGCCATC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.60%	20.40%	0.04%	0.04%	NA
All Indica	2759	74.40%	25.50%	0.07%	0.07%	NA
All Japonica	1512	85.90%	14.10%	0.00%	0.00%	NA
Aus	269	85.50%	14.50%	0.00%	0.00%	NA
Indica I	595	60.00%	39.80%	0.17%	0.00%	NA
Indica II	465	95.50%	4.30%	0.00%	0.22%	NA
Indica III	913	70.30%	29.60%	0.11%	0.00%	NA
Indica Intermediate	786	77.50%	22.40%	0.00%	0.13%	NA
Temperate Japonica	767	94.10%	5.90%	0.00%	0.00%	NA
Tropical Japonica	504	89.10%	10.90%	0.00%	0.00%	NA
Japonica Intermediate	241	53.10%	46.90%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	0.00%	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
vg0115147411	G -> T	LOC_Os01g27170.1	downstream_gene_variant ; 4549.0bp to feature; MODIFIER	silent_mutation	Average:36.792; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0115147411	G -> T	LOC_Os01g27160.1	intron_variant ; MODIFIER	silent_mutation	Average:36.792; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0115147411	G -> DEL	N	N	silent_mutation	Average:36.792; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0115147411	5.15E-10	NA	mr1519	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
vg0115147411	1.29E-08	2.99E-11	mr1519	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
vg0115147411	NA	3.37E-06	mr1519	Jap_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
vg0115147411	NA	7.90E-06	mr1676	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
vg0115147411	NA	7.75E-06	mr1719	Jap_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
vg0115147411	NA	2.34E-07	mr1064_2	Jap_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
vg0115147411	NA	3.19E-06	mr1105_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
vg0115147411	NA	7.97E-06	mr1113_2	Jap_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
vg0115147411	NA	5.72E-07	mr1232_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
vg0115147411	2.63E-17	NA	mr1519_2	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
vg0115147411	3.61E-15	1.77E-24	mr1519_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
vg0115147411	4.76E-06	3.47E-10	mr1519_2	Jap_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
vg0115147411	NA	2.09E-07	mr1745_2	Jap_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