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Detailed information for vg1121619789:

Variant ID: vg1121619789 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21619789
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATGCCTTCATGTATATCGAGGACGAGGTGTCTGCCGTCGTGGGACGAGACGCATTTGAGAAGTACCCCGTTTGGCGCTTTCTTGTATAGATCGTTGCC[G/A]
ACCATACAGTAGATCTTTGCTTTACGGGTTATTTTCTCGGCTTCTGTATCGTCCTCGGGCAACTCCTCGCTGTTGATGAATTTGATTAGTGGGATGCGCC

Reverse complement sequence

GGCGCATCCCACTAATCAAATTCATCAACAGCGAGGAGTTGCCCGAGGACGATACAGAAGCCGAGAAAATAACCCGTAAAGCAAAGATCTACTGTATGGT[C/T]
GGCAACGATCTATACAAGAAAGCGCCAAACGGGGTACTTCTCAAATGCGTCTCGTCCCACGACGGCAGACACCTCGTCCTCGATATACATGAAGGCATAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.90%	0.10%	3.30%	6.67%	NA
All Indica	2759	94.00%	0.20%	1.52%	4.28%	NA
All Japonica	1512	82.70%	0.00%	5.49%	11.84%	NA
Aus	269	98.90%	0.00%	0.37%	0.74%	NA
Indica I	595	93.30%	0.20%	2.18%	4.37%	NA
Indica II	465	94.20%	0.40%	1.08%	4.30%	NA
Indica III	913	94.20%	0.20%	0.88%	4.71%	NA
Indica Intermediate	786	94.30%	0.00%	2.04%	3.69%	NA
Temperate Japonica	767	89.00%	0.00%	2.22%	8.74%	NA
Tropical Japonica	504	74.60%	0.00%	10.52%	14.88%	NA
Japonica Intermediate	241	79.30%	0.00%	5.39%	15.35%	NA
VI/Aromatic	96	69.80%	0.00%	26.04%	4.17%	NA
Intermediate	90	81.10%	0.00%	5.56%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121619789	G -> A	LOC_Os11g36640.1	synonymous_variant ; p.Val1505Val; LOW	synonymous_codon	Average:33.387; most accessible tissue: Minghui63 young leaf, score: 51.901	N	N	N	N
vg1121619789	G -> DEL	LOC_Os11g36640.1	N	frameshift_variant	Average:33.387; most accessible tissue: Minghui63 young leaf, score: 51.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121619789	1.42E-06	NA	mr1603	Ind_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