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Detailed information for vg0605274340:

Variant ID: vg0605274340 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 5274340
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, G: 0.06, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

TAACTATTACAGATATTTGAGTTACTTCAAAATCGCATCGTTTATACTCCCTCCGTACCAAAATAAGTGTAGTTTTTACACTGTTTATGTCTAACGTTTG[G/A]
CTATTCGTCTTATTTAAAAAAATATGTTTAGTATTTTTGTTGTTATTAGATGATAAAACATGAATAGTACTTTATGTGTGACTATTTTTTTTAATTTTTT

Reverse complement sequence

AAAAAATTAAAAAAAATAGTCACACATAAAGTACTATTCATGTTTTATCATCTAATAACAACAAAAATACTAAACATATTTTTTTAAATAAGACGAATAG[C/T]
CAAACGTTAGACATAAACAGTGTAAAAACTACACTTATTTTGGTACGGAGGGAGTATAAACGATGCGATTTTGAAGTAACTCAAATATCTGTAATAGTTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.40%	21.40%	1.18%	0.00%	NA
All Indica	2759	77.30%	21.90%	0.83%	0.00%	NA
All Japonica	1512	83.50%	14.90%	1.59%	0.00%	NA
Aus	269	71.70%	27.10%	1.12%	0.00%	NA
Indica I	595	64.20%	33.80%	2.02%	0.00%	NA
Indica II	465	98.70%	0.90%	0.43%	0.00%	NA
Indica III	913	72.90%	26.90%	0.11%	0.00%	NA
Indica Intermediate	786	79.60%	19.30%	1.02%	0.00%	NA
Temperate Japonica	767	95.80%	2.10%	2.09%	0.00%	NA
Tropical Japonica	504	72.20%	26.80%	0.99%	0.00%	NA
Japonica Intermediate	241	67.60%	31.10%	1.24%	0.00%	NA
VI/Aromatic	96	7.30%	90.60%	2.08%	0.00%	NA
Intermediate	90	71.10%	24.40%	4.44%	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
vg0605274340	G -> A	LOC_Os06g10280.1	downstream_gene_variant ; 2250.0bp to feature; MODIFIER	silent_mutation	Average:58.101; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg0605274340	G -> A	LOC_Os06g10260-LOC_Os06g10280	intergenic_region ; MODIFIER	silent_mutation	Average:58.101; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0605274340	6.57E-24	3.65E-44	mr1201	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
vg0605274340	2.95E-24	5.03E-49	mr1201	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
vg0605274340	3.03E-24	9.51E-38	mr1219	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
vg0605274340	7.69E-24	2.09E-46	mr1219	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
vg0605274340	1.49E-24	1.05E-36	mr1274	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
vg0605274340	3.79E-26	3.06E-44	mr1274	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
vg0605274340	2.92E-24	1.11E-41	mr1201_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
vg0605274340	6.54E-23	1.79E-41	mr1201_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
vg0605274340	8.48E-24	8.20E-39	mr1219_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
vg0605274340	2.41E-22	3.09E-40	mr1219_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
vg0605274340	1.56E-19	4.89E-34	mr1274_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
vg0605274340	3.16E-21	1.60E-40	mr1274_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