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Detailed information for vg1125964996:

Variant ID: vg1125964996 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25964996
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.88, C: 0.13, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

CAGGTTATAAGATGTTTTGACTTTGGTAAAAGTCAAATTACATCAAGTTTGACTAAGTTTATAGACAAATATAGTAATATTTATAATACGAAATTAGTTT[T/C]
ATTAAATCAATAATTGAATATATTTTTATAATAAATTTGTCTTGGGTTAAAAATGTTATTATTTTTTCTACAAACTTAGTCAAACTTAAAACAGTTTAAC

Reverse complement sequence

GTTAAACTGTTTTAAGTTTGACTAAGTTTGTAGAAAAAATAATAACATTTTTAACCCAAGACAAATTTATTATAAAAATATATTCAATTATTGATTTAAT[A/G]
AAACTAATTTCGTATTATAAATATTACTATATTTGTCTATAAACTTAGTCAAACTTGATGTAATTTGACTTTTACCAAAGTCAAAACATCTTATAACCTG

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	62.90%	34.10%	0.25%	2.77%	NA
All Indica	2759	47.60%	47.40%	0.36%	4.68%	NA
All Japonica	1512	93.30%	6.70%	0.00%	0.00%	NA
Aus	269	37.20%	62.50%	0.37%	0.00%	NA
Indica I	595	59.70%	40.20%	0.17%	0.00%	NA
Indica II	465	39.60%	60.00%	0.22%	0.22%	NA
Indica III	913	35.90%	50.80%	0.77%	12.49%	NA
Indica Intermediate	786	56.70%	41.30%	0.13%	1.78%	NA
Temperate Japonica	767	96.90%	3.10%	0.00%	0.00%	NA
Tropical Japonica	504	87.70%	12.30%	0.00%	0.00%	NA
Japonica Intermediate	241	93.40%	6.60%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	60.00%	36.70%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125964996	T -> DEL	N	N	silent_mutation	Average:29.133; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg1125964996	T -> C	LOC_Os11g43040-LOC_Os11g43060	intergenic_region ; MODIFIER	silent_mutation	Average:29.133; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125964996	3.34E-10	6.54E-16	mr1191	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
vg1125964996	1.40E-10	1.87E-11	mr1191	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
vg1125964996	2.79E-13	5.89E-17	mr1644	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
vg1125964996	8.83E-13	2.51E-12	mr1644	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
vg1125964996	6.92E-14	1.27E-21	mr1191_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
vg1125964996	6.40E-12	3.83E-13	mr1191_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