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Detailed information for vg1127362220:

Variant ID: vg1127362220 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27362220
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGAGCAGGGCATGGCGATCACCGACTGTCATGGTTCGGGTTCGGGATGACGGTGTCCATTGCGGGACAATCGGCAAGTCCCTCTCGCTGTCCCATTCAAT[G/T]
GTGCAAGATGTCCAGTCCTGACCAGGCAACATGGAATTATCATTAATGTCTCAGAAATATTTATTTATTTGGAAATGATCATGTTGTAAATAAACCCTTA

Reverse complement sequence

TAAGGGTTTATTTACAACATGATCATTTCCAAATAAATAAATATTTCTGAGACATTAATGATAATTCCATGTTGCCTGGTCAGGACTGGACATCTTGCAC[C/A]
ATTGAATGGGACAGCGAGAGGGACTTGCCGATTGTCCCGCAATGGACACCGTCATCCCGAACCCGAACCATGACAGTCGGTGATCGCCATGCCCTGCTCG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.30%	2.30%	0.38%	15.98%	NA
All Indica	2759	91.20%	2.40%	0.11%	6.38%	NA
All Japonica	1512	65.60%	2.90%	0.73%	30.75%	NA
Aus	269	64.30%	0.00%	1.49%	34.20%	NA
Indica I	595	82.20%	1.50%	0.34%	15.97%	NA
Indica II	465	98.30%	0.20%	0.00%	1.51%	NA
Indica III	913	92.40%	5.70%	0.00%	1.86%	NA
Indica Intermediate	786	92.20%	0.40%	0.13%	7.25%	NA
Temperate Japonica	767	66.90%	5.60%	0.65%	26.86%	NA
Tropical Japonica	504	58.50%	0.00%	1.19%	40.28%	NA
Japonica Intermediate	241	76.30%	0.40%	0.00%	23.24%	NA
VI/Aromatic	96	91.70%	0.00%	0.00%	8.33%	NA
Intermediate	90	84.40%	0.00%	0.00%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127362220	G -> T	LOC_Os11g45210.1	synonymous_variant ; p.Thr103Thr; LOW	synonymous_codon	Average:34.946; most accessible tissue: Callus, score: 73.508	N	N	N	N
vg1127362220	G -> DEL	LOC_Os11g45210.1	N	frameshift_variant	Average:34.946; most accessible tissue: Callus, score: 73.508	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127362220	3.70E-06	5.31E-07	mr1693_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