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Detailed information for vg1123670478:

Variant ID: vg1123670478 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23670478
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAGACTCTGTAGTTTTCTCATTTCATTAATGAAATGGGAGAGGTTTATCCTCTCCTTCTAAAAAAAGGGGTGATAATGGGTGATAAAAAGAATTGATCG[C/T]
GCTGCAGGTGCCCAAATGGGTGATAAAAAGAATTGATCGCTTTTGGAGATCCTTCCTTTGGAAAGGAGAAGACCCTGACAAAACCAACCCGGGCAGCAGT

Reverse complement sequence

ACTGCTGCCCGGGTTGGTTTTGTCAGGGTCTTCTCCTTTCCAAAGGAAGGATCTCCAAAAGCGATCAATTCTTTTTATCACCCATTTGGGCACCTGCAGC[G/A]
CGATCAATTCTTTTTATCACCCATTATCACCCCTTTTTTTAGAAGGAGAGGATAAACCTCTCCCATTTCATTAATGAAATGAGAAAACTACAGAGTCTTT

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	83.20%	8.70%	0.78%	7.32%	NA
All Indica	2759	86.50%	1.90%	0.69%	10.91%	NA
All Japonica	1512	78.20%	19.90%	0.99%	0.93%	NA
Aus	269	96.70%	0.70%	0.00%	2.60%	NA
Indica I	595	90.10%	3.90%	0.67%	5.38%	NA
Indica II	465	76.80%	0.20%	1.72%	21.29%	NA
Indica III	913	87.60%	0.40%	0.11%	11.83%	NA
Indica Intermediate	786	88.30%	3.10%	0.76%	7.89%	NA
Temperate Japonica	767	88.30%	9.30%	1.04%	1.43%	NA
Tropical Japonica	504	65.50%	33.50%	0.99%	0.00%	NA
Japonica Intermediate	241	72.60%	25.30%	0.83%	1.24%	NA
VI/Aromatic	96	33.30%	49.00%	0.00%	17.71%	NA
Intermediate	90	80.00%	8.90%	3.33%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1123670478	C -> T	LOC_Os11g39720-LOC_Os11g39730	intergenic_region ; MODIFIER	silent_mutation	Average:28.266; most accessible tissue: Callus, score: 59.418	N	N	N	N
vg1123670478	C -> DEL	N	N	silent_mutation	Average:28.266; most accessible tissue: Callus, score: 59.418	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123670478	NA	9.83E-10	mr1580	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