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Detailed information for vg0612270091:

Variant ID: vg0612270091 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 12270091
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.02, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

AATTACTCTTTTCTTGAATATCGGGATATTACTATTTTTTGTCCCCGTGTTCAAATGCTAAGTGCAGATGTCAACTTTGATATATATATCTGCTCGGTAT[T/C]
ATTTACACTTGTGTGTGACGTTCCTTGGGCAATAATATTATTGGTTTAATTTTCTTTATGTATTGCGTAAGAAGGTTTCGTATATAGACGCAGGGGTTCT

Reverse complement sequence

AGAACCCCTGCGTCTATATACGAAACCTTCTTACGCAATACATAAAGAAAATTAAACCAATAATATTATTGCCCAAGGAACGTCACACACAAGTGTAAAT[A/G]
ATACCGAGCAGATATATATATCAAAGTTGACATCTGCACTTAGCATTTGAACACGGGGACAAAAAATAGTAATATCCCGATATTCAAGAAAAGAGTAATT

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	50.60%	49.40%	0.06%	0.00%	NA
All Indica	2759	23.80%	76.10%	0.07%	0.00%	NA
All Japonica	1512	98.30%	1.70%	0.07%	0.00%	NA
Aus	269	36.40%	63.60%	0.00%	0.00%	NA
Indica I	595	10.60%	89.40%	0.00%	0.00%	NA
Indica II	465	16.30%	83.70%	0.00%	0.00%	NA
Indica III	913	33.20%	66.80%	0.00%	0.00%	NA
Indica Intermediate	786	27.50%	72.30%	0.25%	0.00%	NA
Temperate Japonica	767	97.90%	2.10%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.20%	0.41%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	62.20%	37.80%	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
vg0612270091	T -> C	LOC_Os06g21230.1	upstream_gene_variant ; 3387.0bp to feature; MODIFIER	silent_mutation	Average:34.264; most accessible tissue: Minghui63 root, score: 55.188	N	N	N	N
vg0612270091	T -> C	LOC_Os06g21220-LOC_Os06g21230	intergenic_region ; MODIFIER	silent_mutation	Average:34.264; most accessible tissue: Minghui63 root, score: 55.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0612270091	NA	3.53E-17	mr1118	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
vg0612270091	NA	6.63E-19	mr1242	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
vg0612270091	NA	9.58E-10	mr1242	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
vg0612270091	NA	7.09E-20	mr1118_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
vg0612270091	NA	4.46E-23	mr1242_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
vg0612270091	NA	1.49E-07	mr1242_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
vg0612270091	NA	4.08E-22	mr1495_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
vg0612270091	NA	1.21E-13	mr1496_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