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Detailed information for vg1118132551:

Variant ID: vg1118132551 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 18132551
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

CGGCAGACAAGTCAGCCAGCAGTGAAGACGAAGACGCCCAGTAACGGCGACAGAGTTGTGCAGCCATGGCAGTGAAATAATCAATCGATAACAGATGAGG[C/T]
ACCCAGTGAAGAAAACGAAGACGCCCATCAGTAGAGGCATAATAAGCCAGCCGTGAAAGCGAAGACACCATGGGCAGCGGCGGAGGCAAGCCAGTGGTAA

Reverse complement sequence

TTACCACTGGCTTGCCTCCGCCGCTGCCCATGGTGTCTTCGCTTTCACGGCTGGCTTATTATGCCTCTACTGATGGGCGTCTTCGTTTTCTTCACTGGGT[G/A]
CCTCATCTGTTATCGATTGATTATTTCACTGCCATGGCTGCACAACTCTGTCGCCGTTACTGGGCGTCTTCGTCTTCACTGCTGGCTGACTTGTCTGCCG

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	85.90%	5.20%	1.16%	7.68%	NA
All Indica	2759	82.90%	3.00%	1.92%	12.21%	NA
All Japonica	1512	98.40%	0.20%	0.00%	1.39%	NA
Aus	269	39.40%	59.50%	0.74%	0.37%	NA
Indica I	595	65.90%	1.30%	2.86%	29.92%	NA
Indica II	465	92.00%	2.20%	1.51%	4.30%	NA
Indica III	913	87.20%	4.30%	1.75%	6.79%	NA
Indica Intermediate	786	85.40%	3.20%	1.65%	9.80%	NA
Temperate Japonica	767	97.40%	0.40%	0.00%	2.22%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	95.60%	0.00%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1118132551	C -> T	LOC_Os11g31140.1	upstream_gene_variant ; 2740.0bp to feature; MODIFIER	silent_mutation	Average:38.489; most accessible tissue: Minghui63 young leaf, score: 69.4	N	N	N	N
vg1118132551	C -> T	LOC_Os11g31150.1	intron_variant ; MODIFIER	silent_mutation	Average:38.489; most accessible tissue: Minghui63 young leaf, score: 69.4	N	N	N	N
vg1118132551	C -> DEL	N	N	silent_mutation	Average:38.489; most accessible tissue: Minghui63 young leaf, score: 69.4	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1118132551	NA	2.36E-08	mr1262	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
vg1118132551	3.43E-07	2.87E-08	mr1425	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