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Detailed information for vg0506060649:

Variant ID: vg0506060649 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 6060649
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

AAAATATTATGAGACCCATTTGTCATTCACATAAAAAAAAATTGTTTGACCCTTGACATGCGGGGCCCACGTGTCATCCTCTCTCCTTCCCTCTTTTGTC[C/T]
TCCCTCTCTCCCTTCTCTCTCCTCTCCCCACGCCGGCATCATGGAGCCCAGCCTAGCCGGTCCTTGCACGCGTAGCTCCAGAAGAGAGTGTAGCAGAAGT

Reverse complement sequence

ACTTCTGCTACACTCTCTTCTGGAGCTACGCGTGCAAGGACCGGCTAGGCTGGGCTCCATGATGCCGGCGTGGGGAGAGGAGAGAGAAGGGAGAGAGGGA[G/A]
GACAAAAGAGGGAAGGAGAGAGGATGACACGTGGGCCCCGCATGTCAAGGGTCAAACAATTTTTTTTTATGTGAATGACAAATGGGTCTCATAATATTTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.90%	6.90%	3.62%	0.57%	NA
All Indica	2759	84.20%	9.20%	5.65%	0.94%	NA
All Japonica	1512	99.00%	0.30%	0.66%	0.00%	NA
Aus	269	99.30%	0.40%	0.00%	0.37%	NA
Indica I	595	82.50%	7.40%	9.08%	1.01%	NA
Indica II	465	76.80%	19.10%	3.87%	0.22%	NA
Indica III	913	87.30%	6.10%	5.15%	1.42%	NA
Indica Intermediate	786	86.30%	8.30%	4.71%	0.76%	NA
Temperate Japonica	767	98.70%	0.30%	1.04%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	32.30%	65.60%	2.08%	0.00%	NA
Intermediate	90	92.20%	4.40%	3.33%	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
vg0506060649	C -> T	LOC_Os05g10920.1	upstream_gene_variant ; 371.0bp to feature; MODIFIER	silent_mutation	Average:71.716; most accessible tissue: Zhenshan97 young leaf, score: 85.184	N	N	N	N
vg0506060649	C -> T	LOC_Os05g10920-LOC_Os05g10930	intergenic_region ; MODIFIER	silent_mutation	Average:71.716; most accessible tissue: Zhenshan97 young leaf, score: 85.184	N	N	N	N
vg0506060649	C -> DEL	N	N	silent_mutation	Average:71.716; most accessible tissue: Zhenshan97 young leaf, score: 85.184	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0506060649	3.58E-10	NA	mr1039	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
vg0506060649	8.69E-07	1.22E-15	mr1039	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
vg0506060649	2.69E-08	NA	mr1039_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
vg0506060649	NA	3.80E-13	mr1039_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
vg0506060649	NA	8.12E-06	mr1125_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
vg0506060649	6.44E-11	NA	mr1632_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
vg0506060649	3.99E-08	1.39E-12	mr1632_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