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Detailed information for vg1105861771:

Variant ID: vg1105861771 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5861771
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

TCAACATGCTAAAATTGTAGGCATGGAGATAACTTTCAATGAATTTCACTCACATAGGCAAACTTTACAACTTATAACTTTTTTGTTGTCATTGGCAGTT[T/C]
TCTAAATTTATAGCGGGTAGTATATATGCTTTTAGACAACAGAATATGTTTCTTTTTTTTTTACATCACTGGCTTCTATATCAGAAATATACGCAAATAC

Reverse complement sequence

GTATTTGCGTATATTTCTGATATAGAAGCCAGTGATGTAAAAAAAAAAGAAACATATTCTGTTGTCTAAAAGCATATATACTACCCGCTATAAATTTAGA[A/G]
AACTGCCAATGACAACAAAAAAGTTATAAGTTGTAAAGTTTGCCTATGTGAGTGAAATTCATTGAAAGTTATCTCCATGCCTACAATTTTAGCATGTTGA

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	97.60%	2.30%	0.06%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.04%	0.00%	NA
All Japonica	1512	93.10%	6.90%	0.00%	0.00%	NA
Aus	269	98.50%	1.10%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.30%	0.13%	0.00%	NA
Temperate Japonica	767	97.90%	2.10%	0.00%	0.00%	NA
Tropical Japonica	504	86.30%	13.70%	0.00%	0.00%	NA
Japonica Intermediate	241	92.10%	7.90%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	2.20%	1.11%	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
vg1105861771	T -> C	LOC_Os11g10670-LOC_Os11g10710	intergenic_region ; MODIFIER	silent_mutation	Average:38.907; most accessible tissue: Callus, score: 83.846	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105861771	NA	4.99E-07	mr1236	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
vg1105861771	1.25E-06	7.71E-12	mr1248	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