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Detailed information for vg1104365050:

Variant ID: vg1104365050 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 4365050
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

TAAGTGAAACCTCATGACAAGTTTAAGGACTGCTATGTGCATTTTACTCTTTAATCTATATGGGTGGTCCTTATAGCTATGGATTTCTAATGCCACCTCT[C/T]
ACAATGGTAAATGTACCCATATGAAGTTATAAGAACTGTTTTTTTTTTCACATTGTGGATGCCCTAATGTGGGTACGCCCATTATCATACAGGAGTAGTA

Reverse complement sequence

TACTACTCCTGTATGATAATGGGCGTACCCACATTAGGGCATCCACAATGTGAAAAAAAAAACAGTTCTTATAACTTCATATGGGTACATTTACCATTGT[G/A]
AGAGGTGGCATTAGAAATCCATAGCTATAAGGACCACCCATATAGATTAAAGAGTAAAATGCACATAGCAGTCCTTAAACTTGTCATGAGGTTTCACTTA

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	97.00%	2.80%	0.21%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	90.80%	8.50%	0.66%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	82.30%	16.40%	1.30%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg1104365050	C -> T	LOC_Os11g08285-LOC_Os11g08290	intergenic_region ; MODIFIER	silent_mutation	Average:44.091; most accessible tissue: Callus, score: 68.286	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1104365050	NA	7.25E-07	mr1062	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
vg1104365050	NA	2.79E-07	mr1585	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
vg1104365050	2.01E-06	6.35E-10	mr1062_2	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