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Detailed information for vg1125315215:

Variant ID: vg1125315215 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25315215
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.74, C: 0.26, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

ATAAATCCCATTGATAATAATATTCGATATTTAAAATCTCAATGGCAATCAAAAGGAGAAGCAGCAGACGGGGTGTATAGGAGTGTAGTTGCAGAGCCGC[T/C]
GACGGTTGGCGAGACTTCTAGAAAATAAAAAATAAAAAATGAATTCTAATGATAATTATGTTCGACTTTTAGAATCCCAATGACAATAAAGAGTAGGCGG

Reverse complement sequence

CCGCCTACTCTTTATTGTCATTGGGATTCTAAAAGTCGAACATAATTATCATTAGAATTCATTTTTTATTTTTTATTTTCTAGAAGTCTCGCCAACCGTC[A/G]
GCGGCTCTGCAACTACACTCCTATACACCCCGTCTGCTGCTTCTCCTTTTGATTGCCATTGAGATTTTAAATATCGAATATTATTATCAATGGGATTTAT

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	47.90%	16.10%	1.50%	34.49%	NA
All Indica	2759	70.80%	3.60%	1.16%	24.47%	NA
All Japonica	1512	14.70%	35.40%	0.33%	49.47%	NA
Aus	269	18.60%	21.60%	10.78%	49.07%	NA
Indica I	595	44.40%	4.70%	2.35%	48.57%	NA
Indica II	465	63.90%	1.90%	2.37%	31.83%	NA
Indica III	913	87.20%	3.60%	0.33%	8.87%	NA
Indica Intermediate	786	75.70%	3.80%	0.51%	19.97%	NA
Temperate Japonica	767	3.30%	54.90%	0.13%	41.72%	NA
Tropical Japonica	504	31.50%	9.90%	0.60%	57.94%	NA
Japonica Intermediate	241	16.20%	27.00%	0.41%	56.43%	NA
VI/Aromatic	96	1.00%	53.10%	3.12%	42.71%	NA
Intermediate	90	42.20%	17.80%	2.22%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125315215	T -> DEL	N	N	silent_mutation	Average:38.086; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg1125315215	T -> C	LOC_Os11g42060.1	downstream_gene_variant ; 654.0bp to feature; MODIFIER	silent_mutation	Average:38.086; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg1125315215	T -> C	LOC_Os11g42050-LOC_Os11g42060	intergenic_region ; MODIFIER	silent_mutation	Average:38.086; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125315215	8.27E-07	8.31E-07	mr1703_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