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Detailed information for vg1108715769:

Variant ID: vg1108715769 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 8715769
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATATCGTTTCATTGTTTATTCATGTGTAGGTGAGTCTTGATTCCTCCGAAGAGCAATGCCAGTGATGAATCGGGAGTCAACATAGGAGAAGATGGCATT[C/A]
AGAAGATCAGGATATCATGCAGGATGATTAGATTAAAGATTGTTGCACATGGTTGGTGAAGATTCCGTATGTCATACCTTGGAGATATTGTGTGTTTATG

Reverse complement sequence

CATAAACACACAATATCTCCAAGGTATGACATACGGAATCTTCACCAACCATGTGCAACAATCTTTAATCTAATCATCCTGCATGATATCCTGATCTTCT[G/T]
AATGCCATCTTCTCCTATGTTGACTCCCGATTCATCACTGGCATTGCTCTTCGGAGGAATCAAGACTCACCTACACATGAATAAACAATGAAACGATATC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.70%	3.50%	2.39%	16.38%	NA
All Indica	2759	70.50%	0.40%	3.08%	25.99%	NA
All Japonica	1512	86.20%	10.10%	1.59%	2.12%	NA
Aus	269	97.00%	0.00%	0.37%	2.60%	NA
Indica I	595	91.80%	0.00%	1.34%	6.89%	NA
Indica II	465	55.10%	0.00%	6.24%	38.71%	NA
Indica III	913	67.70%	0.20%	1.10%	31.00%	NA
Indica Intermediate	786	66.90%	1.10%	4.83%	27.10%	NA
Temperate Japonica	767	96.10%	2.00%	1.96%	0.00%	NA
Tropical Japonica	504	73.00%	23.80%	1.39%	1.79%	NA
Japonica Intermediate	241	82.60%	7.10%	0.83%	9.54%	NA
VI/Aromatic	96	92.70%	0.00%	0.00%	7.29%	NA
Intermediate	90	82.20%	2.20%	3.33%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1108715769	C -> A	LOC_Os11g15390.1	downstream_gene_variant ; 635.0bp to feature; MODIFIER	silent_mutation	Average:20.926; most accessible tissue: Callus, score: 64.918	N	N	N	N
vg1108715769	C -> A	LOC_Os11g15390-LOC_Os11g15400	intergenic_region ; MODIFIER	silent_mutation	Average:20.926; most accessible tissue: Callus, score: 64.918	N	N	N	N
vg1108715769	C -> DEL	N	N	silent_mutation	Average:20.926; most accessible tissue: Callus, score: 64.918	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1108715769	NA	8.01E-09	mr1236	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
vg1108715769	NA	9.28E-09	mr1951	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